A conceptual framework for the dynamic modeling of time-resolved phenotypes for sets of genotype-environment-management combinations: a model library.

Introduction: Dynamic crop growth models are an important tool to predict complex traits, like crop yield, for modern and future genotypes in their current and evolving environments, as those occurring under climate change. Phenotypic traits are the result of interactions between genetic, environmental, and management factors, and dynamic models are designed to generate the interactions producing phenotypic changes over the growing season. Crop phenotype data are becoming increasingly available at various levels of granularity, both spatially (landscape) and temporally (longitudinal, time-series) from proximal and remote sensing technologies. Methods: Here we propose four phenomenological process models of limited complexity based on differential equations for a coarse description of focal crop traits and environmental conditions during the growing season. Each of these models defines interactions between environmental drivers and crop growth (logistic growth, with implicit growth restriction, or explicit restriction by irradiance, temperature, or water availability) as a minimal set of constraints without resorting to strongly mechanistic interpretations of the parameters. Differences between individual genotypes are conceptualized as differences in crop growth parameter values. Results: We demonstrate the utility of such low-complexity models with few parameters by fitting them to longitudinal datasets from the simulation platform APSIM-Wheat involving in silico biomass development of 199 genotypes and data of environmental variables over the course of the growing season at four Australian locations over 31 years. While each of the four models fits well to particular combinations of genotype and trial, none of them provides the best fit across the full set of genotypes by trials because different environmental drivers will limit crop growth in different trials and genotypes in any specific trial will not necessarily experience the same environmental limitation. Discussion: A combination of low-complexity phenomenological models covering a small set of major limiting environmental factors may be a useful forecasting tool for crop growth under genotypic and environmental variation.

Emerging forest-peatland bistability and resilience of European peatland carbon stores.

Northern peatlands store large amounts of carbon. Observations indicate that forests and peatlands in northern biomes can be alternative stable states for a range of landscape settings. Climatic and hydrological changes may reduce the resilience of peatlands and forests, induce persistent shifts between these states, and release the carbon stored in peatlands. Here, we present a dynamic simulation model constrained and validated by a wide set of observations to quantify how feedbacks in water and carbon cycling control resilience of both peatlands and forests in northern landscapes. Our results show that 34% of Europe (area) has a climate that can currently sustain existing rainwater-fed peatlands (raised bogs). However, raised bog initiation and restoration by water conservation measures after the original peat soil has disappeared is only possible in 10% of Europe where the climate allows raised bogs to initiate and outcompete forests. Moreover, in another 10% of Europe, existing raised bogs (concerning ∼20% of the European raised bogs) are already affected by ongoing climate change. Here, forests may overgrow peatlands, which could potentially release in the order of 4% (∼24 Pg carbon) of the European soil organic carbon pool. Our study demonstrates quantitatively that preserving and restoring peatlands requires looking beyond peatland-specific processes and taking into account wider landscape-scale feedbacks with forest ecosystems.

Interventions for medically unexplained symptoms in the emergency department: a critical literature review.

Medically unexplained symptoms, defined as physical symptoms for which no organic pathology can be found, represent 4% of all emergency department attendances annually. The standard management of these patients involves extensive investigation to rule out organic pathology, followed by simple reassurance. We conducted a literature review to determine if there was any intervention that could improve these patient's symptoms and reduce emergency department attendances. A search of MEDLINE, EMBASE and PsycINFO yielded 1612 unique citations, of which six studies met inclusion criteria. The studies were heterogeneous in terms of the participants involved, interventions tested and conclusions drawn. Three studies tested cognitive behavioural therapy, with two finding a reduction in emergency department attendance. Overall, evidence regarding interventions for patients with medically unexplained symptoms in the emergency department is limited and of a variable quality, despite comprising 4% of emergency department attendances. Further research is required to determine the best intervention for this challenging patient group.

Spatial early warning signals for impending regime shifts: A practical framework for application in real-world landscapes.

Prediction of ecosystem response to global environmental change is a pressing scientific challenge of major societal relevance. Many ecosystems display nonlinear responses to environmental change, and may even undergo practically irreversible 'regime shifts' that initiate ecosystem collapse. Recently, early warning signals based on spatiotemporal metrics have been proposed for the identification of impending regime shifts. The rapidly increasing availability of remotely sensed data provides excellent opportunities to apply such model-based spatial early warning signals in the real world, to assess ecosystem resilience and identify impending regime shifts induced by global change. Such information would allow land-managers and policy makers to interfere and avoid catastrophic shifts, but also to induce regime shifts that move ecosystems to a desired state. Here, we show that the application of spatial early warning signals in real-world landscapes presents unique and unexpected challenges, and may result in misleading conclusions when employed without careful consideration of the spatial data and processes at hand. We identify key practical and theoretical issues and provide guidelines for applying spatial early warning signals in heterogeneous, real-world landscapes based on literature review and examples from real-world data. Major identified issues include (1) spatial heterogeneity in real-world landscapes may enhance reversibility of regime shifts and boost landscape-level resilience to environmental change (2) ecosystem states are often difficult to define, while these definitions have great impact on spatial early warning signals and (3) spatial environmental variability and socio-economic factors may affect spatial patterns, spatial early warning signals and associated regime shift predictions. We propose a novel framework, shifting from an ecosystem perspective towards a landscape approach. The framework can be used to identify conditions under which resilience assessment with spatial remotely sensed data may be successful, to support well-informed application of spatial early warning signals, and to improve predictions of ecosystem responses to global environmental change.

Focal laser ablation as clinical treatment of prostate cancer: report from a Delphi consensus project.

PURPOSE: To define the role of focal laser ablation (FLA) as clinical treatment of prostate cancer (PCa) using the Delphi consensus method. METHODS: A panel of international experts in the field of focal therapy (FT) in PCa conducted a collaborative consensus project using the Delphi method. Experts were invited to online questionnaires focusing on patient selection and treatment of PCa with FLA during four subsequent rounds. After each round, outcomes were displayed, and questionnaires were modified based on the comments provided by panelists. Results were finalized and discussed during face-to-face meetings. RESULTS: Thirty-seven experts agreed to participate, and consensus was achieved on 39/43 topics. Clinically significant PCa (csPCa) was defined as any volume Grade Group 2 [Gleason score (GS) 3+4]. Focal therapy was specified as treatment of all csPCa and can be considered primary treatment as an alternative to radical treatment in carefully selected patients. In patients with intermediate-risk PCa (GS 3+4) as well as patients with MRI-visible and biopsy-confirmed local recurrence, FLA is optimal for targeted ablation of a specific magnetic resonance imaging (MRI)-visible focus. However, FLA should not be applied to candidates for active surveillance and close follow-up is required. Suitability for FLA is based on tumor volume, location to vital structures, GS, MRI-visibility, and biopsy confirmation. CONCLUSION: Focal laser ablation is a promising technique for treatment of clinically localized PCa and should ideally be performed within approved clinical trials. So far, only few studies have reported on FLA and further validation with longer follow-up is mandatory before widespread clinical implementation is justified.

A New Statistical Method to Determine the Degree of Validity of Health Economic Model Outcomes against Empirical Data.

BACKGROUND: The validation of health economic (HE) model outcomes against empirical data is of key importance. Although statistical testing seems applicable, guidelines for the validation of HE models lack guidance on statistical validation, and actual validation efforts often present subjective judgment of graphs and point estimates. OBJECTIVES: To discuss the applicability of existing validation techniques and to present a new method for quantifying the degrees of validity statistically, which is useful for decision makers. METHODS: A new Bayesian method is proposed to determine how well HE model outcomes compare with empirical data. Validity is based on a pre-established accuracy interval in which the model outcomes should fall. The method uses the outcomes of a probabilistic sensitivity analysis and results in a posterior distribution around the probability that HE model outcomes can be regarded as valid. RESULTS: We use a published diabetes model (Modelling Integrated Care for Diabetes based on Observational data) to validate the outcome "number of patients who are on dialysis or with end-stage renal disease." Results indicate that a high probability of a valid outcome is associated with relatively wide accuracy intervals. In particular, 25% deviation from the observed outcome implied approximately 60% expected validity. CONCLUSIONS: Current practice in HE model validation can be improved by using an alternative method based on assessing whether the model outcomes fit to empirical data at a predefined level of accuracy. This method has the advantage of assessing both model bias and parameter uncertainty and resulting in a quantitative measure of the degree of validity that penalizes models predicting the mean of an outcome correctly but with overly wide credible intervals.

Assessment of toxicity of selenium and cadmium selenium quantum dots: A review.

This paper reviews the current understanding of the toxicity of selenium (Se) to terrestrial mammalian and aquatic organisms. Adverse biological effects occur in the case of Se deficiencies, associated with this element having essential biological functions and a narrow window between essentiality and toxicity. Several inorganic species of Se (-2, 0, +4, and +6) and organic species (monomethylated and dimethylated) have been reported in aquatic systems. The toxicity of Se in any given sample depends not only on its speciation and concentration, but also on the concomitant presence of other compounds that may have synergistic or antagonistic effects, affecting the target organism as well, usually spanning 2 or 3 orders of magnitude for inorganic Se species. In aquatic ecosystems, indirect toxic effects, linked to the trophic transfer of excess Se, are usually of much more concern than direct Se toxicity. Studies on the toxicity of selenium nanoparticles indicate the greater toxicity of chemically generated selenium nanoparticles relative to selenium oxyanions for fish and fish embryos while oxyanions of selenium have been found to be more highly toxic to rats as compared to nano-Se. Studies on polymer coated Cd/Se quantum dots suggest significant differences in toxicity of weathered vs. non-weathered QD's as well as a significant role for cadmium with respect to toxicity.

Multiparametric MRI/ultrasound fusion-guided biopsy decreases detection of indolent cancer in African-American men.

BACKGROUND: Analysis of systematic 12-core biopsies (SBx) has shown that African-American (AA) men tend to harbor higher risk prostate cancer (PCa) at presentation relative to other races. Multiparametric magnetic resonance imaging (mpMRI) and MRI-ultrasound fusion-guided biopsy (FBx) have been shown to diagnose more intermediate- and high-risk PCa in the general population; however, the efficacy in AA remains largely uncharacterized. We aim to evaluate the utility of FBx in an AA patient cohort. METHODS: Men suspected of PCa underwent an mpMRI and FBx with concurrent SBx from 2007 to 2015 in this institutional review board-approved prospective cohort study. Patient demographics, imaging and fusion biopsy variables were collected. χ2, Mann-Whitney U-test and McNemar's tests were performed to compare proportions, means and paired variables, respectively. Clinically significant PCa (CSPCa) was defined as Gleason score ⩾3+4. RESULTS: Fusion biopsy demonstrated exact agreement with SBx risk categories in 64% of AA men. There was no statistically significant difference in the detection of CSPCa between FBx vs SBx (68 vs 62 cases, P=0.36). However, FBx detected 41% fewer cases of clinically insignificant PCa (CIPCa) compared with SBx (FBx 30 vs SBx 51 cases, P=0.0004). The combined FBx/SBx biopsy approach detected significantly more cases of CSPCa (FBx/SBx 80 vs SBx 62 cases, P=0.004) while detecting comparable number of cases of CIPCa (FBx/SBx 45 vs SBx 51 cases, P=0.37) compared with SBx alone. FBx/SBx also detected more CSPCa in patients with a history of prior negative SBx (FBx/SBx 28 vs 19 cases, P=0.003). CONCLUSIONS: FBx when used in combination with SBx detected more cases of CSPCa while not significantly increasing the diagnosis of CIPCa in AA men. Future multicenter studies will be needed to validate ultimately the clinical implications of FBx in AA patients.

The prostate cancer prevention trial risk calculator 2.0 performs equally for standard biopsy and MRI/US fusion-guided biopsy.

BACKGROUND: The Prostate Cancer Prevention Trial Risk Calculator 2.0 (PCPTRC) is a widely used risk-based calculator used to assess a man's risk of prostate cancer (PCa) before biopsy. This risk calculator was created from data of a patient cohort undergoing a 6-core sextant biopsy, and subsequently validated in men undergoing 12-core systematic biopsy (SBx). The accuracy of the PCPTRC has not been studied in patients undergoing magnetic resonance imaging/ultrasound (MRI/US) fusion-guided biopsy (FBx). We sought to assess the performance of the PCPTRC for straitifying PCa risk in a FBx cohort. METHODS: A review of a prospective cohort undergoing MRI and FBx/SBx was conducted. Data from consecutive FBx/SBx were collected between August 2007 and February 2014, and PCPTRC scores using the PCPTRC2.0R-code were calculated. The risk of positive biopsy and high-grade cancer (Gleason ⩾7) on biopsy was calculated and compared with overall and high-grade cancer detection rates (CDRs). Receiver operating characteristic curves were generated and the areas under the curves (AUCs) were compared using DeLong's test. RESULTS: Of 595 men included in the study, PCa was detected in 39% (232) by SBx compared with 48% (287) on combined FBx/SBx biopsy. The PCPTRC AUCs for the CDR were similar (P=0.70) for SBx (0.69) and combined biopsy (0.70). For high-grade disease, AUCs for SBx (0.71) and combined biopsy (0.70) were slightly higher, but were not statistically different (P=0.55). CONCLUSIONS: In an MRI-screened population of men undergoing FBx, PCPTRC continues to represent a practical method of accurately stratifying PCa risk.

Resilience through adaptation.

Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs) provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover's distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system.

Utilization of multiparametric prostate magnetic resonance imaging in clinical practice and focal therapy: report from a Delphi consensus project.

PURPOSE: To codify the use of multiparametric magnetic resonance imaging (mpMRI) for the interrogation of prostate neoplasia (PCa) in clinical practice and focal therapy (FT). METHODS: An international collaborative consensus project was undertaken using the Delphi method among experts in the field of PCa. An online questionnaire was presented in three consecutive rounds and modified each round based on the comments provided by the experts. Subsequently, a face-to-face meeting was held to discuss and finalize the consensus results. RESULTS: mpMRI should be performed in patients with prior negative biopsies if clinical suspicion remains, but not instead of the PSA test, nor as a stand-alone diagnostic tool or mpMRI-targeted biopsies only. It is not recommended to use a 1.5 Tesla MRI scanner without an endorectal or pelvic phased-array coil. mpMRI should be performed following standard biopsy-based PCa diagnosis in both the planning and follow-up of FT. If a lesion is seen, MRI-TRUS fusion biopsies should be performed for FT planning. Systematic biopsies are still required for FT planning in biopsy-naïve patients and for patients with residual PCa after FT. Standard repeat biopsies should be taken during the follow-up of FT. The final decision to perform FT should be based on histopathology. However, these consensus statements may differ for expert centers versus non-expert centers. CONCLUSIONS: The mpMRI is an important tool for characterizing and targeting PCa in clinical practice and FT. Standardization of acquisition and reading should be the main priority to guarantee consistent mpMRI quality throughout the urological community.

The Missing Stakeholder Group: Why Patients Should be Involved in Health Economic Modelling.

Evaluations of healthcare interventions, e.g. new drugs or other new treatment strategies, commonly include a cost-effectiveness analysis (CEA) that is based on the application of health economic (HE) models. As end users, patients are important stakeholders regarding the outcomes of CEAs, yet their knowledge of HE model development and application, or their involvement therein, is absent. This paper considers possible benefits and risks of patient involvement in HE model development and application for modellers and patients. An exploratory review of the literature has been performed on stakeholder-involved modelling in various disciplines. In addition, Dutch patient experts have been interviewed about their experience in, and opinion about, the application of HE models. Patients have little to no knowledge of HE models and are seldom involved in HE model development and application. Benefits of becoming involved would include a greater understanding and possible acceptance by patients of HE model application, improved model validation, and a more direct infusion of patient expertise. Risks would include patient bias and increased costs of modelling. Patient involvement in HE modelling seems to carry several benefits as well as risks. We claim that the benefits may outweigh the risks and that patients should become involved.

A fast fan-beam backprojection algorithm based on efficient sampling.

We introduce a fast algorithm to backproject fan-beam tomographic projections. For typical configurations of computed tomography scanners, the algorithm reduces the number of computations and actual runtimes by an order of magnitude. Similar to fast algorithms for the parallel-beam geometry, this algorithm is a divide-and-conquer method that aggregates the projections in a hierarchical manner. The computational speedup results from the use of sparse sampling grids to represent images that are comprised of a small number of projections that are close together in view-angle. In the parallel beam case these sparse (Cartesian) sampling grids were constructed by exploiting the projection slice theorem. Extending the parallel beam algorithms to fan-beam is a significant step because there is no equivalent to the projection-slice theorem for the fan-beam geometry. This was achieved using a novel analysis of fan-beam backprojection that characterizes the spatially-varying frequency content. This analysis, which we present here, allows for the construction and use of the sparse (non-Cartesian) sampling grids.

Ferrate(VI) oxidation of propranolol: kinetics and products.

The oxidation of propranolol (PPL), a ß-blocker by ferrate(VI) (Fe(VI)) was studied by performing kinetics, stoichiometry, and analysis of the reaction products. The rate law for the oxidation of PPL by Fe(VI) was first-order with respect to each reactant. The dependence of second-order rate constants of the reaction of Fe(VI) and PPL on pH was explained using acid-base equilibrium of Fe(VI) and PPL. The required molar stoichiometry for the complete removal of PPL was determined to be 6:1 ([Fe(VI)]:[PPL]). The identified products using liquid chromatography-tandem mass spectrometry were oxidized product (OP)-292, OP-308, and OP-282. The formed OPs could possibly compete with the parent molecule to react with Fe(VI) and thus resulted in a non-linear relationship between degradation of PPL and the added amount of Fe(VI). Rate and removal studies indicate the Fe(VI) is able to oxidize PPL and hence can also oxidize other ß-blockers, e.g., atenolol and metoprolol.

Kinetics of the oxidation of sucralose and related carbohydrates by ferrate(VI).

The kinetics of the oxidation of sucralose, an emerging contaminant, and related monosaccharides and disaccharides by ferrate(VI) (Fe(VI)) were studied as a function of pH (6.5-10.1) at 25°C. Reducing sugars (glucose, fructose, and maltose) reacted faster with Fe(VI) than did the non-reducing sugar sucrose or its chlorinated derivative, sucralose. Second-order rate constants of the reactions of Fe(VI) with sucralose and disaccharides decreased with an increase in pH. The pH dependence was modeled by considering the reactivity of species of Fe(VI), (HFeO(4)(-) and FeO(4)(2-)) with the studied substrates. Second-order rate constants for the reaction of Fe(VI) with monosaccharides displayed an unusual variation with pH and were explained by considering the involvement of hydroxide in catalyzing the ring opening of the cyclic form of the carbohydrate at increased pH. The rate constants for the reactions of carbohydrates with Fe(VI) were compared with those for other oxidant species used in water treatment and were briefly discussed.

Oxidation of trimethoprim by ferrate(VI): kinetics, products, and antibacterial activity.

Kinetics, stoichiometry, and products of the oxidation of trimethoprim (TMP), one of the most commonly detected antibacterial agents in surface waters and municipal wastewaters, by ferrate(VI) (Fe(VI)) were determined. The pH dependent second-order rate constants of the reactions of Fe(VI) with TMP were examined using acid-base properties of Fe(VI) and TMP. The kinetics of reactions of diaminopyrimidine (DAP) and trimethoxytoluene (TMT) with Fe(VI) were also determined to understand the reactivity of Fe(VI) with TMP. Oxidation products of the reactions of Fe(VI) with TMP and DAP were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Reaction pathways of oxidation of TMP by Fe(VI) are proposed to demonstrate the cleavage of the TMP molecule to ultimately result in 3,4,5,-trimethoxybenzaldehyde and 2,4-dinitropyrimidine as among the final identified products. The oxidized products mixture exhibited no antibacterial activity against E. coli after complete consumption of TMP. Removal of TMP in the secondary effluent by Fe(VI) was achieved.

Self-assembly of Silver Nanoparticles and Multiwall Carbon Nanotubes on Decomposed GaAs Surfaces.

Atomic Force Microscopy complemented by Photoluminescence and Reflection High Energy Electron Diffraction has been used to study self-assembly of silver nanoparticles and multiwall carbon nanotubes on thermally decomposed GaAs (100) surfaces. It has been shown that the decomposition leads to the formation of arsenic plate-like structures. Multiwall carbon nanotubes spin coated on the decomposed surfaces were mostly found to occupy the depressions between the plates and formed boundaries. While direct casting of silver nanoparticles is found to induce microdroplets. Annealing at 300°C was observed to contract the microdroplets into combined structures consisting of silver spots surrounded by silver rings. Moreover, casting of colloidal suspension consists of multiwall carbon nanotubes and silver nanoparticles is observed to cause the formation of 2D compact islands. Depending on the multiwall carbon nanotubes diameter, GaAs/multiwall carbon nanotubes/silver system exhibited photoluminescence with varying strength. Such assembly provides a possible bottom up facile way of roughness controlled fabrication of plasmonic systems on GaAs surfaces.

Food quality in producer-grazer models: a generalized analysis.

Stoichiometric constraints play a role in the dynamics of natural populations but are not explicitly considered in most mathematical models. Recent theoretical works suggest that these constraints can have a significant impact and should not be neglected. However, it is not yet resolved how stoichiometry should be integrated in population dynamical models, as different modeling approaches are found to yield qualitatively different results. Here we investigate a unifying framework that reveals the differences and commonalities between previously proposed models for producer-grazer systems. Our analysis reveals that stoichiometric constraints affect the dynamics mainly by increasing the intraspecific competition between producers and by introducing a variable biomass conversion efficiency. The intraspecific competition has a strongly stabilizing effect on the system, whereas the variable conversion efficiency resulting from a variable food quality is the main determinant for the nature of the instability once destabilization occurs. Only if the food quality is high can an oscillatory instability, as in the classical paradox of enrichment, occur. While the generalized model reveals that the generic insights remain valid in a large class of models, we show that other details such as the specific sequence of bifurcations encountered in enrichment scenarios can depend sensitively on assumptions made in modeling stoichiometric constraints.