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High‐frequency heating processes are widely used in industry, for example, for food processing, wood drying, or plastic welding. A recent development in this field uses radio‐frequency heating to fuse particle foam beads to complex components. The aim of using the modified process is to reduce the energy consumption of particle foam fusion. Within this process, the molds used must be electrically insulating to ensure the building of an electrical field. For this purpose, mold made of two different plastics were analyzed. Additional to the dielectric, mechanical, and thermal expansion, the thermal conductivity of the mold materials are of great interest. Although welding is finished quickly, cooling to the demolding temperature is comparably long. To achieve shorter cooling and therefore shorter process times, the mold materials were modified by two different thermal conductive but electrically insulating fillers. By the use of the thermally optimized mold materials, a reduction in cooling time of up to 40% was possible. At the same time, the heating step was hardly affected. Mechanical properties were enhanced while thermal expansion was reduced.

The disparate nature of data for electric power utilities complicates the emergency recovery and response process. The reduced efficiency of response to natural hazards and disasters can extend the time that electrical service is not available for critical end-use loads, and in extreme events, leave the public without power for extended periods. This article presents a methodology for the development of a semantic data model for power systems and the integration of electrical grid topology, population, and electric distribution line reliability indices into a unified, cloud-based, serverless framework that supports power system operations in response to extreme events. An iterative and pragmatic approach to working with large and disparate datasets of different formats and types resulted in improved application runtime and efficiency, which is important to consider in real time decision-making processes during hurricanes and similar catastrophic events. This technology was developed initially for Puerto Rico, following extreme hurricane and earthquake events in 2017 and 2020, but is applicable to utilities around the world. Given the highly abstract and modular design approach, this technology is equally applicable to any geographic region and similar natural hazard events. In addition to a review of the requirements, development, and deployment of this framework, technical aspects related to application performance and response time are highlighted.

The steam chest molding process is currently state of the art concerning the generation of three‐dimensional polymeric foam components made from particle foams. An adaption of the high‐frequency welding process shows advantages regarding the required energy and the used water. Due to the low dielectric loss factors of the most common foam materials (PE, PP, and PS), they cannot be heated sufficiently by an electric field. To enable heating of these foams, the particles may be coated with a second material that shows a high dielectric loss. The possible heat development of the modified particles was simulatively investigated. To ensure a realistic simulation, the properties of the used materials are analyzed beforehand. The heating simulation shows clear dependence regarding the particle size and the shell thickness. By a suitable combination, sufficient heating is achievable. For single particles, an irregular temperature distribution is calculated, mainly caused by the difference of permittivity resulting in a local variation of electrical flux density. Bigger particles and thicker shells will result in faster heating ramps and higher overall temperatures. The additional calculation regarding a particle–particle interaction shows a homogenization of the temperature distribution across the particle surface.

In recent years, the demand for polymer compound solutions for the application of bipolar plates in polymer electrolyte membrane fuel cells (PEMFC) has increased continuously due to significant cost and lifetime advantages compared to metallic solutions. The main challenge of the compounds is the high filler content required to ensure sufficient electrical conductivity of the bipolar plates. The associated increase in viscosity and simultaneously increased thermal conductivity limit the conventional injection molding process in terms of achievable flow path length to wall thickness ratios (plate aspect ratio). In order to evaluate the extent to which highly modified electrically conductive polymer material systems can be processed into thin-walled and highly dimensionally stable bipolar plates, an injection compression molding process with dynamic mold temperature control (ICM-DT) has been developed. For this purpose, a compound was prepared from polypropylene (PP) and graphite-flakes. The compound was characterized with respect to the achieved filler content, the electrical conductivity, as well as the pressure- and temperature-dependent solidification range. The ICM-DT experiments were carried out by varying the maximum mold temperature and the compression force. In addition, the process was designed with multiple compression and decompression steps to account for a possible pressure-dependent solidification of the compound. The plates were characterized with respect to the achieved plate aspect ratio and the flow-path-dependent dimensional thickness stability. It was shown that the plate aspect ratio could be increased by up to 125% with the maximum filler content compared to conventional injection molding processes provided in the literature. With the multi-stage ICM-DT process, it was also possible to optimize the thickness dimensional stability with a maximum deviation of 3% over the flow path.

During evolution, genomes are shaped by a plethora of forces that can leave characteristic signatures. A common goal when studying diverging populations is to detect the signatures of selective sweeps, which can be rather difficult in complex demographic scenarios, such as under secondary contact. Moreover, the detection of selective sweeps, especially in whole-genome data, often relies heavily on a narrow set of summary statistics that are affected by a multitude of factors, frequently leading to false positives and false negatives. Simulating genomic regions makes it possible to control these demographic and population genetic factors. We used simulations of large genomic regions to determine how different secondary contact and sympatric speciation scenarios affect the footprint of hard and soft selective sweeps in the presence of varying degrees of gene flow and recombination. We explored the ability of an array of population genetic summary statistics to detect the footprints of these selective sweeps under specific demographies. We focussed on metrics that do not require phased data or ancestral sequences and therefore have wide applicability. We found that a newly developed beta diversity measure

Purpose: 7-ketocholesterol (7kCh), a natural byproduct of oxidation in lipoprotein deposits is implicated in the pathogenesis of diabetic retinopathy and age-related macular degeneration (AMD). This study was performed to investigate whether several clinical drugs can inhibit 7kCh-induced caspase activation and mitigate its apoptotic effects on retinal cells in vitro. Method: Two populations of retinal cells, human retinal pigment epithelial cells (ARPE-19) and rat neuroretinal cells (R28) were exposed to 7kCh in the presence of the following inhibitors: Z-VAD-FMK (pan-caspase inhibitor), simvastatin, memantine, epicatechin, and Z-IETD-FMK (caspase-8 inhibitor) or Z-ATAD-FMK (caspase-12 inhibitor). Caspase-3/7, -8, and -12 activity levels were measured by fluorochrome caspase assays to quantify cell death. IncuCyte live-cell microscopic images were obtained to quantify cell counts. Results: Exposure to 7kCh for 24 hours significantly increased caspase activities for both ARPE-19 and R28 cells (P < 0.05). In ARPE cells, pretreatment with various drugs had significantly lower caspase-3/7, -8, and -12 activities, reported in % change in mean signal intensity (msi): Z-VAD-FMK (48% decrease, P < 0.01), memantine (decreased 47.8% at 1 µM, P = 0.0039 and 81.9% at 1 mM, P < 0.001), simvastatin (decreased 85.3% at 0.01 µM, P < 0.001 and 84.8% at 0.05 µM, P < 0.001) or epicatechin (83.6% decrease, P < 0.05), Z-IETD-FMK (68.1% decrease, P < 0.01), and Z-ATAD-FMK (47.7% decrease, P = 0.0017). In contrast, R28 cells exposed to 7kCh continued to have elevated caspase-3/7, -8, and -12 activities (between 25.7% decrease and 17.5% increase in msi, P > 0.05) regardless of the pretreatment. Conclusion: Several current drugs protect ARPE-19 cells but not R28 cells from 7kCh-induced apoptosis, suggesting that a multiple-drug approach is needed to protect both cells types in various retinal diseases.

Traditional benchmarking implicitly assumes that decision making units operate in isolation from their peers. For arable production systems in particular, this assumption is unlikely to hold in reality. This paper quantifies spatial spillovers on input‐specific inefficiency using data envelopment analysis and a second‐stage bootstrap truncated regression model. The bootstrap algorithm is extended to allow for the estimation of the parameter of the spatial weight matrix, which captures the proximity between producers. The empirical application concerns Dutch arable farms for which latitudes and longitudes are available. The average inefficiency across years was 3.87% for productive inputs and 2.98% for damage abatement inputs under variable returns to scale. For productive inputs technical inefficiency, statistically significant spillover effects from neighbours’ age and their degree of specialisation depended on the type of the spatial weight matrix used (inverse distance or k‐nearest neighbours). Statistically significant spillover effects of subsidy payments were adverse while statistically significant spillover effects from insurance payments were beneficial. For damage abatement inputs technical inefficiency, statistically significant adverse effects were found for neighbours’ age and subsidy payments and beneficial effects from neighbours’ insurance payments and their degree of specialisation.

Expandable graphite (EG) and graphite (G) were assessed as multifunctional additives improving both flame retardancy and thermal conductivity in highly filled, thermal conductive polymeric materials based on polyamide 6 (PA6). Fire testing was conducted using modern UL-94, LOI and cone calorimeter test setups. It is demonstrated that thermal conductivity can significantly influence the time to ignition, although offering little fire resistance once ignited even in highly filled systems. Thus, for PA6 formulations containing solely 70 wt.% G, the peak heat release rate (pHRR) measured in cone calorimeter tests was 193 kW/m², whereas PA6 formulations containing 20 wt.% EG/50 wt.% G did not exhibit a measurable heat development. Particular attention was paid to effect separation between thermal conductivity and residue formation. Good thermal conductivity properties are proven to be particularly effective in test scenarios where the heat impact is comparatively low and the testing environment provides good heat dissipation and convective cooling possibilities. For candle-like ignition scenarios (e.g., LOI), filling levels of >50 wt.% (G or EG/G) are shown to be sufficient to suppress ignition exclusively by thermal conductivity. V0 classifications in UL-94 vertical burning tests were achieved for PA6 formulations containing ≥70 wt.% G, ≥25 wt.% EG and ≥20 wt.% EG/25 wt.% G.

Software developers often look for solutions to their code-level problems using the Stack Overflow Q&A website. To receive help, developers frequently submit questions containing sample code segments and the description of the programming issue. Unfortunately, it is not always possible to reproduce the issues from the code segments that may impede questions from receiving prompt and appropriate solutions. We conducted an exploratory study on the reproducibility of issues discussed in 400 Java and 400 Python questions. We parsed, compiled, executed, and carefully examined the code segments from these questions to reproduce the reported programming issues. The outcomes of our study are three-fold. First, we found that we can reproduce approximately 68% of Java and 71% of Python issues, whereas we were unable to reproduce approximately 22% of Java and 19% of Python issues using the code segments. Of the issues that were reproducible, approximately 67% of the Java code segments and 20% of the Python code segments required minor or major modifications to reproduce the issues. Second, we carefully investigated why programming issues could not be reproduced and provided evidence-based guidelines for writing effective code examples for Stack Overflow questions. Third, we investigated the correlation between the issue reproducibility status of questions and the corresponding answer meta-data, such as the presence of an accepted answer. According to our analysis, a reproducible question has at least two times higher chance of receiving an accepted answer than an irreproducible question. Besides, the median time delay in receiving accepted answers is double if the issues reported in questions could not be reproduced. We also investigate the confounding factors (e.g., reputation) and find that confounding factors do not hurt the correlation between reproducibility status and answer meta-data., This study has been accepted for publication in Empirical Software Engineering EMSE) journal

Fisheries induce one of the strongest anthropogenic selective pressures on natural populations, but the genetic effects of fishing remain unclear. Crucially, we lack knowledge of how capture-associated selection and its interaction with reductions in population density caused by fishing can potentially shift which genes are under selection. Using experimental fish reared at two densities and repeatedly harvested by simulated trawling, we show consistent phenotypic selection on growth, metabolism, and social behavior regardless of density. However, the specific genes under selection—mainly related to brain function and neurogenesis—varied with the population density. This interaction between direct fishing selection and density could fundamentally alter the genomic responses to harvest. The evolutionary consequences of fishing are therefore likely context dependent, possibly varying as exploited populations decline. These results highlight the need to consider environmental factors when predicting effects of human-induced selection and evolution.

Data visualization is integral for exploratory data analysis and data presentation. Consequently, every programming environment suitable for data analysis needs a feature-rich visualization library. In this paper, we present Plotly.NET - a fully featured charting library for the .NET ecosystem. Plotly.NET requires little ceremony to use, provides multiple API (application programming interface) layers for both low-code and maximum customizability, and can be used in many different visualization workflows - from interactive scripting and notebooks to user interface applications. Plotly.NET brings the charting capabilities of plotly.js to the .NET ecosystem, successfully combining the flexibility of the plotly grammar with the type-safety and expressiveness of .NET.

Matrix targeting sequences (MTSs) direct proteins from the cytosol into mitochondria. Efficient targeting often relies on internal matrix targeting-like sequences (iMTS-Ls) which share structural features with MTSs. Predicting iMTS-Ls was tedious and required multiple tools and webservices. We present iMLP, a deep learning approach for the prediction of iMTS-Ls in protein sequences. A recurrent neural network has been trained to predict iMTS-L propensity profiles for protein sequences of interest. The iMLP predictor considerably exceeds the speed of existing approaches. Expanding on our previous work on iMTS-L prediction, we now serve an intuitive iMLP webservice available at http://iMLP.bio.uni-kl.de and a stand-alone command line tool for power user in addition.

Differences in technical efficiency across farms are one of the major factors explaining differences in farm survival and growth and changes in farm industry structure. This study employs Data Envelopment Analysis (DEA) to compute technical inefficiency scores for output, energy, materials, pesticides and fertiliser of a sample of Dutch indoor vegetable farms within the period 2006–2016. A bootstrap truncated regression model is used to determine statistical associations between producer-specific characteristics and technical inefficiency scores for the specified inputs. For the sample of indoor growers, the average technical inefficiency was about 14% for energy, 23% for materials, 24% for pesticides and 22% for fertilisers. The bootstrap truncated regression suggested that the degree of specialisation exerts adverse effects on the technical inefficiency of variable inputs. While age, short-term, long-term debt and subsidy were statistically significant, the coefficients were not economically significant. Building the capacity of farmers to reduce input inefficiency will enable farmers to be competitive and reduce the adverse effects of input overuse on the environment.

The introduction of Xylella fastidiosa in Apulia has resulted in the desiccation of millions of olive trees. Here, we employ a multi-country partial equilibrium model to analyze the possible distribution of economic impacts among olive oil processors and consumers. The results suggest that the majority of the impacts would fall on consumers as a consequence of higher prices. If the disease disperses beyond the current extent in Italy the decline in consumer welfare ranges from 4.1 billion to 10.3 billion Euro over the course of 50 years depending on the rate of disease spread. In other words, each of the 195 million households in Europe would incur additional costs ranging 63 cents to 1.6 Euro every year over the course of 50 years. Introductions of the pathogen into Greece or Spain could cost European consumers between 0.4 billion to 3.3 billion Euro and 1.8 billion to 53 billion Euro, respectively. This would correspond to additional annual household costs ranging 6 to 51 cents and 27 cents to 8.2 Euro, respectively. As significant economic consequences from further dispersal of the disease are borne by consumers, the economic threat is not limited to producers but should be contextualized as a societal problem.

Analyses of the economic impact of, and possible risk mitigation strategies against, pests often fail to account for spatial and economic dependencies among the evaluated decision-making units, and heterogeneity in the environment they operate in. Awareness of the mutual dependence of actors, regions and countries is critical for proper management of pests. In this thesis, I develop methodological approaches to account for the spatial nature of pest populations and the mutual dependence of farmers, countries, and markets to contribute to a more informed discussion on plant health policies in Europe.Chapter 2 provides an empirical approach to measure spatial spillover effects of decision-making units’ characteristics with managerial performance of neighbors. This allows relaxing the assumption that decision-making units operate in isolation from their peers. The model is applied to data from the Farm Accountancy Data Network. The data comprises expenses, revenues, balance sheet positions, and farm characteristics for 75 Dutch arable crop farms which are observed over six years. The results show that managerial performance of decision-making units is related to neighbors’ characteristics such as the degree of farm specialization, received subsidies, insurance payments, and age. However, how they associate is found to depend on the definition of the neighborhood. The results imply that analyses of optimal pest control should be expanded beyond individual farm-level.Chapter 3 provides an integrated framework that derives insights from climatic suitability, spread modelling, and economic modelling. A pest spread model is developed such that environmental heterogeneity, point of pest introduction, and host locations are fundamental components for the realized dispersal over time. The economic model captures heterogeneity of different cropping systems and countries, includes temporal effects through losses in investments, and highlights economic dependence among growers due to price responses following changes in aggregate supply. The model is applied to the invasive species Xylella fastidiosa subspecies pauca to compute impacts to olive growers in Europe, with a focus on Italy, Greece, and Spain. For Italy, across the considered spread rates the potential economic impact over 50 years ranges from 1.9 billion to 5.2 billion Euros for the economic worst-case scenario, in which production ceases after orchards die off. If replanting with resistant varieties is feasible, the impact ranges from 0.6 billion to 1.6 billion Euros. Even under slow spread rates and the ability to replant with resistant cultivars, economic impact to olive growers from further spread of Xylella fastidiosa subspecies pauca is expected to be sizable (0.6 billion Euro) and warrants strong regulatory response.Chapter 4 translates results of the spatially explicit pest spread model to suit the needs of partial equilibrium models. The chapter shows how global sensitivity analyses can be informative in the context of partial equilibrium models. The model is applied to the invasive species Xylella fastidiosa subspecies pauca to compute impacts on producers and consumers of olive oil in Europe, with a particular focus on Italy, Greece, and Spain. I find that most of the potential future impact of Xylella fastidiosa subspecies pauca in the olive oil market would fall on consumers because of higher prices following reductions in supply. The analysis highlights that the problem of invasive pests should be contextualized as a societal challenge as opposed to one that affects only producers. The chapter stresses the fact that consumers are beneficiaries of pest control.Chapter 5 shows that a joint analysis of several hundred pests can produce hotspot maps with a high accuracy. A machine learning model is trained on a dataset covering 248 invasive species to map risk of new pest introduction in Europe as a function of climate, soils, water, and anthropogenic factors. Due to the considerable time and labor requirements for species-specific analyses, there is no information on area-specific suitability for establishment or introduction for many hazardous species. The joint analysis of several species could be one approach for addressing this knowledge gap. Furthermore, joint analyses of various pests could help to identify weak-links and thereby inform collective control. Results show that the BeNeLux states, Northern Italy, the Northern Balkans, and the United Kingdom, and areas around container ports such as Antwerp, London, Rijeka, and Saint Petersburg are at higher risk for introductions. However, harmonized, systematic, species survey data comprising also true absences are required to further validate and improve these maps.The thesis, as a collection of these articles, contributes to the literature by providing methodological approaches which (i) capture spatial dependencies, (ii) account for environmental and economic heterogeneity at the level of granularity feasible under the available data, (iii) acknowledge the temporal nature of pest spread and economic impact in perennial hosts, (iv) highlight the actionable insights sensitivity analyses can generate, and (v) propose cost-effective modelling strategies to address the absence of risk maps for many invasive species.

Our goal was to explore the detrimental impacts of ciprofloxacin (CPFX) and tetracycline (TETRA) on human retinal Müller (MIO-M1) cells in vitro. Cells were exposed to 30, 60 and 120 μg/ml of CPFX and TETRA. The cellular metabolism was measured with the MTT assay. The JC-1 and CM-H2DCFDA assays were used to evaluate the levels of mitochondrial membrane potential (MMP) and ROS (reactive oxygen species), respectively. Mitochondrial DNA (mtDNA) copy number, along with gene expression levels associated with apoptotic (BAX, BCL2-L13, BCL2, CASP-3 and CASP-9), inflammatory (IL-6, IL-1β, TGF-α, TGF-β1 and TGF-β2) and antioxidant pathways (SOD2, SOD3, GPX3 and NOX4) were analyzed via Quantitative Real-Time PCR (qRT-PCR). Bioenergetic profiles were measured using the Seahorse® XF Flux Analyzer. Cells exposed 24 h to 120 μg/ml TETRA demonstrated higher cellular metabolism compared to vehicle-treated cells. At each time points, (i) all TETRA concentrations reduced MMP levels and (ii) ROS levels were reduced by TETRA 120 μg/ml treatment. TETRA caused (i) higher expression of CASP-3, CASP-9, TGF-α, IL-1B, GPX3 and SOD3 but (ii) decreased levels of TGF-B2 and SOD2. ATP production and spare respiratory capacity declined with TETRA treatment. Cellular metabolism was reduced with CPFX 120 μg/ml in all cultures and 60 μg/ml after 72 h. The CPFX 120 μg/ml reduced MMP in all cultures and ROS levels (72 h). CPFX treatment (i) increased expression of CASP-3, CASP-9, and BCL2-L13, (ii) elevated the basal oxygen consumption rate, and (iii) lowered the mtDNA copy numbers and expression levels of TGF-B2, IL-6 and IL-1B compared to vehicle-control cells. We conclude that clinically relevant dosages of bactericidal and bacteriostatic antibiotics can have negative effects on the cellular metabolism and mitochondrial membrane potential of the retinal MIO-M1 cells in vitro. It is noteworthy to mention that apoptotic and inflammatory pathways in exposed cells were affected significantly This is the first study showing the negative impact of fluoroquinolones and tetracyclines on mitochondrial behavior of human retinal MIO-M1 cells.

BackgroundDrug therapy yields different results depending on its recipient population. Cisplatin, a commonly used chemotherapeutic agent, causes different levels of resistance and side effects for different patients, but the mechanism(s) are presently unknown. It has been assumed that this variation is a consequence of differences in nuclear (n) DNA, epigenetics, or some external factor(s). There is accumulating evidence that an individual’s mitochondrial (mt) DNA may play a role in their response to medications. Variations within mtDNA can be observed, and an individual’s mtDNA can be categorized into haplogroups that are defined by accumulations of single nucleotide polymorphisms (SNPs) representing different ethnic populations.MethodsThe present study was conducted on transmitochondrial cytoplasmic hybrids (cybrids) that possess different maternal-origin haplogroup mtDNA from African (L), Hispanic [A+B], or Asian (D) backgrounds. Cybrids were created by fusing Rho0 ARPE-19 cells (lacking mtDNA) with platelets, which contain numerous mitochondria but no nuclei. These cybrid cells were cultured to passage five, treated with cisplatin, incubated for 48 h, then analyzed for cell metabolic activity (tetrazolium dye (MTT) assay), mitochondrial membrane potential (JC-1 assay), cytotoxicity (lactate dehydrogenase (LDH) assay), and gene expression levels forALK,BRCA1,EGFR, andERBB2/HER2.ResultsResults indicated that untreated cybrids with varying mtDNA haplogroups had similar relative metabolic activity before cisplatin treatment. When treated with cisplatin, (1) the decline in metabolic activity was greatest in L (27.4%,p p = 0.0001) and [A+B] cybrids (24.67%,p = 0.0285) compared to untreated cybrids; (2) mitochondrial membrane potential remained unchanged in all cybrids (3) LDH production varied between cybrids (L >[A+B],p = 0.0270). (4) The expression levels decreased forALKin L (p p = 0.0001) cybrids but not in D cybrids (p = 0.285); and decreased forEGFRin [A+B] cybrids (p = 0.0246) compared to untreated cybrids.ConclusionOur findings suggest that an individual’s mtDNA background may be associated with variations in their response to cisplatin treatment, thereby affecting the efficiency and the severity of side effects from the treatment.

The objective of gene set enrichment analysis (GSEA) in modern biological studies is to identify functional profiles in huge sets of biomolecules generated by high-throughput measurements of genes, transcripts, metabolites, and proteins. GSEA is based on a two-stage process using classical statistical analysis to score the input data and subsequent testing for overrepresentation of the enrichment score within a given functional coherent set. However, enrichment scores computed by different methods are merely statistically motivated and often elusive to direct biological interpretation. Here, we propose a novel approach, called Thermodynamically Motivated Enrichment Analysis (TMEA), to account for the energy investment in biological relevant processes. Therefore, TMEA is based on surprisal analysis, which offers a thermodynamic-free energy-based representation of the biological steady state and of the biological change. The contribution of each biomolecule underlying the changes in free energy is used in a Monte Carlo resampling procedure resulting in a functional characterization directly coupled to the thermodynamic characterization of biological responses to system perturbations. To illustrate the utility of our method on real experimental data, we benchmark our approach on plant acclimation to high light and compare the performance of TMEA with the most frequently used method for GSEA.

Summary Plant metabolism is broadly reprogrammed during acclimation to abiotic changes. Most previous studies have focused on transitions from standard to single stressful conditions. Here, we systematically analyze acclimation processes to levels of light, heat, and cold stress that subtly alter physiological parameters and assess their reversibility during de-acclimation. Metabolome and transcriptome changes were monitored at 11 different time points. Unlike transcriptome changes, most alterations in metabolite levels did not readily return to baseline values, except in the case of cold acclimation. Similar regulatory networks operate during (de-)acclimation to high light and cold, whereas heat and high-light responses exhibit similar dynamics, as determined by surprisal and conditional network analyses. In all acclimation models tested here, super-hubs in conditional transcriptome networks are enriched for components involved in translation, particularly ribosomes. Hence, we suggest that the ribosome serves as a common central hub for the control of three different (de-)acclimation responses., Graphical Abstract, Highlights • Time series of acclimation and de-acclimation without pleiotropic stresses • Kinetics of transcriptomes and metabolomes under three environmental conditions • Transcriptomes return to a baseline, but HL and heat metabolomes do not • All acclimation responses involve the translational machinery and photosynthesis, Biological Sciences; Metabolomics; Plant Biology; Plants; Transcriptomics

Significance Xylella fastidiosa is one of the most dangerous plant-pathogenic bacteria worldwide. Regulatory measures were enacted in response to the detection of the subsp. pauca (Xfp) in Italian olives in 2013, but the current impact is nevertheless major. We developed a spatially explicit bio-economic model to compute potential future economic impact of the Xfp strain. Uncertainty on spread is accounted for by simulating different scenarios. The majority of orchards were found to be within climatically suitable territory. Even under slow disease spread and the ability to replant with resistant cultivars, projections of future economic impact in affected countries run in the billions of Euros. Our findings highlight the importance of minimizing disease spread and implementing adaptation measures in affected areas., Xylella fastidiosa is the causal agent of plant diseases that cause massive economic damage. In 2013, a strain of the bacterium was, for the first time, detected in the European territory (Italy), causing the Olive Quick Decline Syndrome. We simulate future spread of the disease based on climatic-suitability modeling and radial expansion of the invaded territory. An economic model is developed to compute impact based on discounted foregone profits and losses in investment. The model projects impact for Italy, Greece, and Spain, as these countries account for around 95% of the European olive oil production. Climatic suitability modeling indicates that, depending on the suitability threshold, 95.5 to 98.9%, 99.2 to 99.8%, and 84.6 to 99.1% of the national areas of production fall into suitable territory in Italy, Greece, and Spain, respectively. For Italy, across the considered rates of radial range expansion the potential economic impact over 50 y ranges from 1.9 billion to 5.2 billion Euros for the economic worst-case scenario, in which production ceases after orchards die off. If replanting with resistant varieties is feasible, the impact ranges from 0.6 billion to 1.6 billion Euros. Depending on whether replanting is feasible, between 0.5 billion and 1.3 billion Euros can be saved over the course of 50 y if disease spread is reduced from 5.18 to 1.1 km per year. The analysis stresses the necessity to strengthen the ongoing research on cultivar resistance traits and application of phytosanitary measures, including vector control and inoculum suppression, by removing host plants.

Xylella fastidiosa is the causal agent of plant diseases that cause massive economic damage. In 2013, a strain of the bacterium was, for the first time, detected in the European territory (Italy), causing the Olive Quick Decline Syndrome. We simulate future spread of the disease based on climatic-suitability modeling and radial expansion of the invaded territory. An economic model is developed to compute impact based on discounted foregone profits and losses in investment. The model projects impact for Italy, Greece, and Spain, as these countries account for around 95% of the European olive oil production. Climatic suitability modeling indicates that, depending on the suitability threshold, 95.5 to 98.9%, 99.2 to 99.8%, and 84.6 to 99.1% of the national areas of production fall into suitable territory in Italy, Greece, and Spain, respectively. For Italy, across the considered rates of radial range expansion the potential economic impact over 50 y ranges from 1.9 billion to 5.2 billion Euros for the economic worst-case scenario, in which production ceases after orchards die off. If replanting with resistant varieties is feasible, the impact ranges from 0.6 billion to 1.6 billion Euros. Depending on whether replanting is feasible, between 0.5 billion and 1.3 billion Euros can be saved over the course of 50 y if disease spread is reduced from 5.18 to 1.1 km per year. The analysis stresses the necessity to strengthen the ongoing research on cultivar resistance traits and application of phytosanitary measures, including vector control and inoculum suppression, by removing host plants., This work was supported by funding from the EU’s Horizon 2020 Pest Organisms Threatening Europe research and innovation program under Grant 635646. M.C. held an Institut Valencià d’Investigacions Agràries grant partially funded by the European Social Fund Comunitat Valenciana 2014–2020.

BackgroundSalmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the generaSalvelinusandCoregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup.ResultsAll selection analyses are based onCoregonusandSalvelinuscompared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such asap1m2, involved in immunity and development, andslc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genessyn3, with a role in neural processes, andctsk, involved in bone remodelling.ConclusionsOur approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.

In the past decade, anti-vascular endothelial growth factor (VEGF) therapy has become more popular and the standard of care for several retinal diseases including exudative age-related macular degeneration (AMD) (Brown et al., 2006; Martin et al., 2012; Rosenfeld et al., 2006; Tufail et al., 2010), diabetic macular edema (DME) (Brown et al., 2013; Do et al., 2012; Do et al., 2013; TDRCR, 2015), and macular edema (ME) due to retinal vein occlusion (RVO) (Brown et al., 2010; Brown et al., 2013; Campochiaro et al., 2010; Wu et al., 2008). Ranibizumab (Lucentis®, Genentech, San Francisco, CA) is a humanized, recombinant, monoclonal antibody fragment. Intended for intraocular use, a 0.5mg/0.05ml dose is approved by the Food and Drug Administration for exudative AMD and ME due to RVO; a 0.3mg/0.05ml dose is approved by the FDA for DME, and diabetic retinopathy (DR). Bevacizumab (Avastin®, Genentech, San Francisco, CA) is a humanized monoclonal human immunoglobulin gamma 1 (IgG1) antibody that selectively binds to circulating VEGF and inhibit its binding to cell surface receptors. A 1.25mg/0.05ml is used off-label in the United States and is commonly used worldwide for exudative AMD, DME and RVO. Aflibercept (Eylea®, Regeneron Pharmaceuticals, Tarrytown, NY) is a recombinant protein receptor decoy composed of two VEGF receptors 1 and 2 fused with the Fc region of human IgG1. Compared to the former two anti-VEGF drugs, it has a higher binding affinity for VEGF and it also binds to VEGF-B and Placental growth factor (PGF). A concentration of 2.0mg/0.05ml is approved by the FDA for wet AMD, DME, ME due to RVO, and DR in patients with DME. Ziv-aflibercept (Zaltrap®, Sanofi Aventis, Bridgewater, NJ and Regeneron Pharmaceuticals, Tarrytown, NY), also known as VEGF Trap-oncologic, contains 25 mg/ml ziv-aflibercept, however contains higher sucrose concentrations than aflibercept (Eylea), which results in higher osmolality (Bayer, 2014; Group, 2012). Ziv-aflibercept is approved by the FDA for treatment of resistant or progressing metastatic colorectal cancer. However, Mansour et al. (Mansour et al., 2015; Mansour et al., 2017a; Mansour et al., 2017b); de Oliveira Dias et al. (de Oliveira Dias et al., 2015; de Oliveira Dias et al., 2017; de Oliveira Dias et al., 2016); and Chhablani et al., (Chhablani, 2015; Chhablani et al., 2017), among other authors, have published several reports finding good outcomes and no apparent safety issues in a series of patients treated with intravitreal ziv-aflibercept. Previous studies have shown that anti-VEGF drugs in clinically significant doses do not affect cell viability in vitro in a human retinal pigment epithelium (RPE) cell line (ARPE-19) (Luthra et al., 2006; Malik et al., 2014b). Nonetheless, subtle cytotoxic changes in RPE cells, such as decrease in mitochondrial membrane potential, could be observed even at clinical doses for some anti-VEGF drugs (Malik et al., 2014b). Numerous publications have described in vitro differential responses to the different anti-VEGF drugs in various retinal cells (Deissler et al., 2012; Klettner et al., 2010; Schnichels et al., 2013). Muller cells are predominant glial cells in the retina and provide structural and metabolic support to retinal neurons. Several studies have described numerous functions of Muller cells, including regulation of cellular homeostasis and pH, modulation of neurotransmitter recycling, contribution to the blood-retinal barrier by surrounding retinal capillaries with glial processes (Limb et al., 2002; Reichenbach and Bringmann, 2013), acting as light collectors by directing light to photoreceptors (Franze et al., 2007; Reichenbach and Bringmann, 2013), and secretion and regulation of VEGF and pigment epithelium derived factor (PEDF) (Garcia and Vecino, 2003; Limb et al., 2002; Reichenbach and Bringmann, 2013). Muller cells have also been associated with retinal neuroprotection, wound healing and regeneration (Garcia and Vecino, 2003). The purpose of this study was to evaluate the in vitro response and differences in gene expression of human retinal Muller cells treated with different concentrations of ranibizumab, bevacizumab, aflibercept or ziv-aflibercept. Assays for cell viability, metabolic activity, mitochondrial membrane potential (ΔΨm), reactive oxygen species (ROS) and apoptosis were used to evaluate responses to the anti-VEGF drugs. In addition, differences in the expression levels for angiogenesis-related, pro-apoptotic, inflammation and oxidative stress genes were assessed.

Bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix have been two economically important aquaculture species in China for centuries. In the past decades, bighead and silver carp have been introduced from the Yangtze River to many river systems in China, including the Pearl River, in annual, large-scale, stocking activities to enhance wild fisheries. Nonetheless, few studies have assessed the ecological or genetic impacts of such introductions on native conspecific fish populations. An mtDNA D-loop segment of 978 bp from 213 bighead carp samples from 9 populations and a 975 bp segment from 204 silver carp samples from 10 populations were obtained to evaluate genetic diversity and population integrity. Results from a haplotype network analysis revealed that most haplotypes of the Pearl River clustered with those of Yangtze River origin and only a small proportion were distinct, suggesting that both the native Pearl River bighead and silver carp populations are currently dominated by genetic material from the Yangtze River. The genetic diversity of Pearl River populations is high in both species because of this inter-population gene flow, but the diversity of native Pearl River populations is low. To preserve the native genetic diversity, stocking of non-native fingerlings should cease immediately and native Pearl River bighead and silver carp fish farms should be established. This research demonstrates the danger to native biodiversity across China because of the substantial, ongoing stock-enhancement activities without prior genetic assessment.

PurposeIntravitreal injections of anti-vascular endothelial growth factor (VEGF) treatments are currently used to treat wet age-related macular degeneration (AMD), diabetic retinopathy, and macular edema. Chronic, repetitive treatments with anti-VEGF may have unintended consequences beyond the inhibition of angiogenesis. Most recently, clinical trials have been conducted with risuteganib (RSG, Luminate®), which is anti-angiogenic and has neuroprotective and anti-inflammatory properties. Mitochondrial damage and dysfunction play a major role in development of AMD. Transmitochondrial cybrids are cell lines established by fusing human retinal pigment epithelial (RPE) cells that are Rho0 (lacking mtDNA) with platelets isolated from AMD subjects or age-matched normal subjects. Cybrid cell lines have identical nuclei but mitochondria from different subjects, enabling investigation of the functional consequences of damaged AMD mitochondria. The present study compares the responses of AMD cybrids treated with bevacizumab (Bmab, Avastin®) versus risuteganib (RSG, Luminate®).MethodsCybrids were created by fusing mtDNA depleted ARPE-19cells with platelets from AMD or age-matched normal patients. AMD (n=5) and normal (n=3) cybrids were treated for 48h with or without 1x clinical dose of 1.25 mg/50μl (25,000μg/ml) of Bmab or 1.0 mg/50μl (20,000μg/ml) of RSG. Cultures were analyzed for levels of cleaved caspase 3/7 and NucLight Rapid Red staining (IncuCyte® Live Cell Imager), mitochondrial membrane potential (ΔΨm, JC1 assay) or reactive oxygen species (ROS, H2DCFDA assay). Expression levels of genes related to the following pathways were analyzed with qRT-PCR: Apoptosis (BAX, BCL2L13, CASP-3, -7, -9); angiogenesis (VEGFA, HIF1α, PDGF); integrins (ITGB-1, -3, -5, ITGA-3, -5, -V); mitochondrial biogenesis (PGC1α, POLG); oxidative stress (SOD2, GPX3, NOX4); inflammation (IL-6, -18, -1β, IFN-β1); and signaling (P3KCA, PI3KR1). Statistical analyses were performed using GraphPad Prism software.ResultsThe untreated AMD cybrids had significantly higher levels of cleaved caspase 3/7 compared to the untreated normal cybrids. The Bmab-treated AMD cybrids showed elevated levels of cleaved caspase 3/7 compared to untreated AMD or RSG-treated AMD cybrids. The Bmab-treated cybrids had lower ΔΨm compared to untreated AMD or RSG-treated AMD cybrids. The ROS levels were not changed with Bmab or RSG treatment. Results showed that Bmab-treated cybrids had higher expression levels of inflammatory (IL-6, IL1-β), oxidative stress (NOX4) and angiogenesis (VEGFA) genes compared to untreated AMD, while RSG-treated cybrids had lower expression levels of apoptosis (BAX), angiogenesis (VEGFA) and integrin (ITGB1) genes.ConclusionsThese data suggest that the mechanism(s) of action of RSG, an integrin regulator, and Bmab, a recombinant monoclonal antibody, affect the AMD RPE cybrid cells differently, with the former having more anti-apoptosis properties, which may be desirable in treating degenerative ocular diseases.

Mitochondrial (mt) DNA haplogroups, defined by specific single nucleotide polymorphism (SNPs) patterns, represent populations of diverse geographic origins and may play a role in disparate disease susceptibilities found in different ethnic/racial populations. The most common European haplogroup is H, while the K haplogroup is highly associated with Ashkenazi Jewish populations. Studies using transmitochondrial cybrids (cell lines with identical nuclei but mitochondria from either H or K haplogroup subjects) demonstrated significant molecular and biological differences but mechanisms for these disparities are unclear. In this study, we hypothesized that there is differential retrograde signaling occurring between the Stimulator of Interferon Genes (STING) pathway and H versus K mtDNA haplogroups. Results showed that K cybrids exhibit increased levels of cytoplasmic mtDNA fragments. After STING Knock-Down, H cybrids had lower expression levels for EGFR, BRCA1, DNMT3A, DNMT3B, HDAC1, and IFNα genes, but upregulated DNMT3A compared to control H cybrids. The STING-KD K cybrids showed downregulation of EGFR, DNMT3A, HDAC1, HCAD9, CFH, and CHI, along with upregulation of DNMT1 and IL-6 compared to control K cybrids. Since all cybrids have identical nuclei, the STING DNA sensor system interacts differently with K haplogroup mtDNA compared to H mtDNA for genes related to cancer (EGFR, BRCA1), methylation (DNMT1, DNMT3A, DNMT3B), acetylation (HDAC1, HDCA9), complement (CFH, CHI) and inflammation (IFNα, IL-6). In summary, in non-pathologic conditions, (a) STING is an important retrograde signaling mechanism(s) and (b) cybrids possessing Ashkenazi Jewish mtDNA (K haplogroup) interact with the STING complex differently compared to H cybrids which affects various disease-related pathways.

Purpose A critical biological function of retina pigment epithelium (RPE) cells is phagocytosis of photoreceptor outer segment (POS) disc membranes. Mitochondrial damage and dysfunction are associated with RPE cells of age-related macular degeneration (AMD) retinas. In this study, we use a transmitochondrial cybrid model to compare the phagocytic properties of RPE cells that contain AMD mitochondria versus age-matched normal mitochondria and their response to treatment with anti-vascular endothelial growth factor (VEGF) drugs: bevacizumab, ranibizumab, and aflibercept. Methods Cybrids, which are cell lines with identical nuclei but mitochondria (mt) from different subjects, are created by fusing mtDNA depleted ARPE-19 cells with platelets from AMD or age-matched normal patients. AMD (n = 5) and normal (n = 5) cybrids were treated with 1 μm fluorescent latex beads (1.52 × 107 beads/mL) and either 2.09 μM of bevacizumab, 2.59 μM of ranibizumab, or 5.16 μM of aflibercept. These doses of anti-VEGF drugs are equivalent to intravitreal injections given to AMD patients with choroidal neovascularization. Flow cytometry was performed using the ImageStreamX Mark II to assess phagocytic bead-uptake. The average fold values for bead-uptake and SEM were calculated using GraphPad Prism software. Results Normal cybrids showed decreased bead-uptake with a fold value of 0.65 ± 0.103 (p = 0.01) after treatment with bevacizumab, 0.80 ± 0.034 (p = 0.0003) with ranibizumab, and 0.81 ± 0.053 (p = 0.007) with aflibercept compared to the untreated normal cybrids (baseline fold of 1). The bevacizumab-treated, ranibizumab-treated, and aflibercept-treated AMD cybrids had decreased bead-uptake with a fold value of 0.71 ± 0.061 (p = 0.001), 0.70 ± 0.101 (p = 0.02), and 0.74 ± 0.125 (p = 0.07), respectively, compared to the untreated AMD cybrids (baseline fold of 1). Conclusions Our initial findings showed that when treated with bevacizumab and ranibizumab, both AMD cybrids and age-matched normal cybrids had a significant decrease in bead-uptake. A similar decrease in bead-uptake was found in normal cybrids treated with aflibercept and while the AMD values trended lower, they were not significant. This data suggests that anti-VEGF drugs can cause loss of phagocytic function.

Three experiments with male and female rats were conducted to examine the effects of Pavlovian extinction training on Pavlovian-to-instrumental transfer (PIT) in a task in which the unconditioned stimulus (US) was presented at an early time point within an extended conditioned stimulus (CS). Two instrumental responses were trained with different reinforcing outcomes (R1-O1, R2-O2) and then, independently, 2 stimuli were trained with those outcomes (S1-O1, S2-O2). One group then underwent an extinction treatment (S1-, S2-) and a second was merely exposed to the experimental contexts without any stimulus events. Finally, the effects of the 2 stimuli on instrumental responding were assessed in PIT tests. Across experiments we varied the number of Pavlovian training trials prior to extinction (8, 16, or 64 trials) and the length of time following extinction prior to test (i.e., 1 or 21 days, in a test for spontaneous recovery). We observed that outcome-specific PIT was reduced by extinction in all of our training conditions and that this extinction effect was durable, surviving a 3-week spontaneous recovery interval even though conditioned magazine approach spontaneously recovered over this interval. Although extinction reduced the magnitude of PIT, the temporal expression of PIT was mostly unaffected. We found these effects in both male and female rats, though in 1 study females were extinction-resistant. These data suggest that under the conditions studied here Pavlovian extinction may permanently weaken the ability of Pavlovian cues to retrieve a representation of their associated outcomes without impacting the temporal organization of responding. This suggests that different features of learning may be differentially sensitive to extinction. (PsycINFO Database Record