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Abstract Background Phenotypic characterization of transgenic cell lines, frequently used in plant biology studies, is complicated because transgene expression in individual cells is often heterogeneous and unstable. To identify the sources and to reduce this heterogeneity, we transformed tobacco (Nicotiana tabacum L.) BY-2 cells with a gene encoding green fluorescent protein (GFP) using Agrobacterium tumefaciens, and then introduced a simple cloning procedure to generate cell lines derived from the individual transformed cells. Expression of the transgene was monitored by analysing GFP fluorescence in the cloned lines and also in lines obtained directly after transformation. Results The majority (~90%) of suspension culture lines derived from calli that were obtained directly from transformation consisted of cells with various levels of GFP fluorescence. In contrast, nearly 50% of lines generated by cloning cells from the primary heterogeneous suspensions consisted of cells with homogenous GFP fluorescence. The rest of the lines exhibited "permanent heterogeneity" that could not be resolved by cloning. The extent of fluorescence heterogeneity often varied, even among genetically identical clones derived from the primary transformed lines. In contrast, the offspring of subsequent cloning of the cloned lines was uniform, showing GFP fluorescence intensity and heterogeneity that corresponded to the original clone. Conclusion The results demonstrate that, besides genetic heterogeneity detected in some lines, the primary lines often contained a mixture of epigenetically different cells that could be separated by cloning. This indicates that a single integration event frequently results in various heritable expression patterns, which are probably accidental and become stabilized in the offspring of the primary transformed cells early after the integration event. Because heterogeneity in transgene expression has proven to be a serious problem, it is highly advisable to use transgenes tagged with a visual marker for BY-2 transformation. The cloning procedure can be used not only for efficient reduction of expression heterogeneity of such transgenes, but also as a useful tool for studies of transgene expression and other purposes.

Soft elastic composite materials can serve as actuators when they transform changes in external fields into mechanical deformation. Here, we theoretically address the corresponding deformational behavior in model systems of magnetic gels and elastomers exposed to external magnetic fields. In reality, such materials consist of magnetizable colloidal particles in a soft polymeric matrix. Since many practical realizations of such materials involve particulate inclusions of polydisperse size distributions, we concentrate on the effect that mixed particle sizes have on the overall deformational response. To perform a systematic study, our focus is on binary size distributions. We systematically vary the fraction of larger particles relative to smaller ones and characterize the resulting magnetostrictive behavior. The consequences for systems of various different spatial particle arrangements and different degrees of compressibility of the elastic matrix are evaluated. In parts, we observe a qualitative change in the overall response for selected systems of mixed particle sizes. Specifically, overall changes in volume and relative elongations or contractions in response to an induced magnetization can be reversed into the opposite types of behavior. Our results should apply to the characteristics of other soft elastic composite materials like electrorheological gels and elastomers when exposed to external electric fields as well. Overall, we hope to stimulate corresponding experimental realizations and the further investigation on the purposeful use of mixed particle sizes as a means to design tailored requested material behavior. [ABSTRACT FROM AUTHOR]

Abstract Background Tuberization in potato (Solanum tuberosum L.) represents a morphogenetic transition of stolon growth to tuber formation, which is under complex environmental and endogenous regulation. In the present work, we studied the regulatory mechanisms and the role of different morphogenetic factors in a newly isolated potato mutant, which exhibited spontaneous tuberization (ST). The ST mutant was characterized in detail at morphological, physiological and biochemical levels. Results Tuberization of the ST mutant grown in the soil was photoperiod-insensitive; predominantly sessile tubers formed directly from axillary buds even under continuous light. Single-node cuttings of the ST mutant cultured in vitro frequently formed tubers or basal tuber-like swellings instead of normal shoots under conditions routinely used for shoot propagation. The tuberization response of ST cuttings under light was dependent on sucrose, the concentration of which had to exceed certain threshold that inversely correlated with irradiance. Gibberellic acid prevented tuberization of ST cuttings, but failed to restore normal shoot phenotype and caused severe malformations. Carbohydrate analysis showed increased levels of both soluble sugars and starch in ST plants, with altered carbohydrate partitioning and metabolism. Comparative proteomic analysis revealed only a few differences between ST- and wild-type plants, primary amongst which seemed to be the absence of an isoform of manganese-stabilizing protein, a key subunit of photosystem II. Conclusion ST mutant exhibits complex developmental and phenotypic modifications, with features that are typical for plants strongly induced to tuberize. These changes are likely to be related to altered regulation of photosynthesis and carbohydrate metabolism rather than impaired transduction of inhibitory gibberellin or photoperiod-based signals. The effect of gibberellins on tuberization of ST mutant suggests that gibberellins inhibit tuberization downstream of the inductive effects of sucrose and other positive factors.

Fully-automated nuclear image segmentation is the prerequisite to ensure statistically significant, quantitative analyses of tissue preparations,applied in digital pathology or quantitative microscopy. The design of segmentation methods that work independently of the tissue type or preparation is complex, due to variations in nuclear morphology, staining intensity, cell density and nuclei aggregations. Machine learning-based segmentation methods can overcome these challenges, however high quality expert-annotated images are required for training. Currently, the limited number of annotated fluorescence image datasets publicly available do not cover a broad range of tissues and preparations. We present a comprehensive, annotated dataset including tightly aggregated nuclei of multiple tissues for the training of machine learning-based nuclear segmentation algorithms. The proposed dataset covers sample preparation methods frequently used in quantitative immunofluorescence microscopy. We demonstrate the heterogeneity of the dataset with respect to multiple parameters such as magnification, modality, signal-to-noise ratio and diagnosis. Based on a suggested split into training and test sets and additional single-nuclei expert annotations, machine learning-based image segmentation methods can be trained and evaluated. Measurement(s) nucleus • Annotation • Frozen Section • Neuroblastoma • Touch Prep Slide • Centrifuged Smear Slide • cells grown on slide • Ganglioneuroblastoma • Wilms Tumor • HaCaT cell Technology Type(s) Fluorescence Imaging • machine learning Factor Type(s) nucleus segmentation Sample Characteristic - Organism Homo sapiens Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12570854 [ABSTRACT FROM AUTHOR]

Highly oxygenated organic molecules (HOMs) contribute substantially to the formation and growth of atmospheric aerosol particles, which affect air quality, human health and Earth's climate. HOMs are formed by rapid, gas-phase autoxidation of volatile organic compounds (VOCs) such as α -pinene, the most abundant monoterpene in the atmosphere. Due to their abundance and low volatility, HOMs can play an important role in new-particle formation (NPF) and the early growth of atmospheric aerosols, even without any further assistance of other low-volatility compounds such as sulfuric acid. Both the autoxidation reaction forming HOMs and their NPF rates are expected to be strongly dependent on temperature. However, experimental data on both effects are limited. Dedicated experiments were performed at the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber at CERN to address this question. In this study, we show that a decrease in temperature (from +25 to -50 ∘ C) results in a reduced HOM yield and reduced oxidation state of the products, whereas the NPF rates (J1.7nm) increase substantially. Measurements with two different chemical ionization mass spectrometers (using nitrate and protonated water as reagent ion, respectively) provide the molecular composition of the gaseous oxidation products, and a two-dimensional volatility basis set (2D VBS) model provides their volatility distribution. The HOM yield decreases with temperature from 6.2 % at 25 ∘ C to 0.7 % at -50 ∘ C. However, there is a strong reduction of the saturation vapor pressure of each oxidation state as the temperature is reduced. Overall, the reduction in volatility with temperature leads to an increase in the nucleation rates by up to 3 orders of magnitude at -50 ∘ C compared with 25 ∘ C. In addition, the enhancement of the nucleation rates by ions decreases with decreasing temperature, since the neutral molecular clusters have increased stability against evaporation. The resulting data quantify how the interplay between the temperature-dependent oxidation pathways and the associated vapor pressures affect biogenic NPF at the molecular level. Our measurements, therefore, improve our understanding of pure biogenic NPF for a wide range of tropospheric temperatures and precursor concentrations. [ABSTRACT FROM AUTHOR]

Background: The objective of this study was to analyze prognostic factors and risk stratification in patients with pulmonary arterial hypertension (PAH) and comorbidities.Methods: Patients with invasively diagnosed PAH were included in the analysis. Comorbidities were clinically diagnosed as proposed in the 6th World Symposium of pulmonary hypertension. Uni- and multivariate analysis were employed for identification of factors predicting survival and time to first clinical worsening (TTCW). Risk stratification was based on parameters from ESC/ERS-guidelines 2015.Results: In total 142 patients were enrolled in the study, 90 of them were diagnosed as PAH without and 52 with comorbidities. All patients received targeted PAH therapy and were followed for 3.3 ± 2.4 years. In PAH patients without comorbidities survival and TTCW were significantly associated with reduced 6-min walking distance (6MWD), elevated N-terminal pro brain natriuretic peptide (NT-proBNP), WHO-functional class (WHO-FC) and right atrial (RA) area. In the multivariate analysis, 6MWD was an independent predictor for survival (p = 0.002) and WHO-FC for TTCW (p = 0.001). In patients with PAH and comorbidities these parameters had no significant association with survival and TTCW. Average risk score was significantly associated with survival (p = 0.001) and TTCW (p = 0.013) in PAH but not in PAH with comorbidities (both p > 0.05; figure 1).Conclusion: Risk stratification based on ESC/ERS-guidelines could only be confirmed in patients without comorbidities, but not in patients with PAH and comorbidities. The data of this study suggest, that a different risk stratification needs to be applied to PAH patients with comorbidities. Further studies are needed to confirm these results.Trial Registration: Not applicable, retrospective registry. [ABSTRACT FROM AUTHOR]

Highly-oxygenated organic molecules (HOMs) contribute substantially to the formation and growth of atmospheric aerosol particles, which affect air quality, human health and Earth's climate. HOMs are formed by rapid, gas-phase autoxidation of volatile organic compounds (VOCs) such as α-pinene, the most abundant monoterpene in the atmosphere. Due to their abundance and low volatility, HOMs can play an important role for new-particle formation (NPF) and the early growth of atmospheric aerosols, even without any further assistance of other low-volatility compounds such as sulfuric acid. Both the autoxidation reaction forming HOMs and their new-particle formation rates are expected to be strongly dependent on temperature. However, experimental data on both effects are limited. Dedicated experiments were performed at the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber at CERN to address this question. In this study, we show that a decrease in temperature (from +25 to -50 °C) results in a reduced HOM yield and reduced oxidation state of the products, whereas the new-particle formation rates (J1.7 nm) increase substantially. Measurements with two different chemical ionization mass spectrometers (using nitrate and protonated water as reagent ion, respectively) provide the molecular composition of the gaseous oxidation products and a 2-dimensional volatility basis set model (2D-VBS) provides their volatility distribution. The HOM yield decreases with temperature from 6.2 % at 25 °C to 0.7 % at -50 °C. However, there is a strong reduction of the saturation vapor pressure of each oxidation state as the temperature is reduced. Overall, the reduction in volatility with temperature leads to an increase in the nucleation rates by up to three orders of magnitude at -50 °C compared with 25 °C. In addition, the enhancement of the nucleation rates by ions decreases with decreasing temperature, since the neutral molecular clusters have increased stability against evaporation. The resulting data quantify how the interplay between the temperature-dependent oxidation pathways and the associated vapor pressures affect biogenic new-particle formation at the molecular level. Our measurements therefore improve our understanding of pure biogenic new-particle formation for a wide range of tropospheric temperatures and precursor concentrations. [ABSTRACT FROM AUTHOR]

• Neural network RANS GEKO coefficients. • Bayesian optimization. • High turbulence boundary condition. • Novel film cooling designs. • Reduction of hot gas entrainment. In this numerical study an optimized trench film cooling design is determined using a Bayesian algorithm and neural network trained RANS model. Three objective functions were considered, the area-averaged film cooling efficiency, spatial standard deviation of film cooling efficiency and hot gas ingestion into the trench. Nine geometrical design parameters were varied to allow for a 3D trench shape and to find an optimal trench design based on the initial parametrization of the trench. Jet-engine like inflow boundary conditions with respect to turbulence intensity and length scales were applied. The investigated momentum ratios (I) were 1 and 8 at a main flow Reynolds number (R e D) of 2500. For each design the steady state Reynolds Averaged Navier-Stokes (RANS) equations were solved using the commercial Computational Fluid Dynamics (CFD) code Ansys Fluent V2022 R1. The turbulence model coefficients of the generalized k − ω (GEKO) model were tuned to approximate the time-averaged 3D temperature field from a predictive Large Eddy Simulation (LES) and trained by a neural network to improve the prediction capability. The tuned GEKO model shows improved agreement with experimental data of a literature case compared to the standard GEKO model. With this tuned RANS model optimized trench designs are found and validated by additional LES's. The optimized designs include angled side walls to improve former trench designs, particularly in mitigating hot gas entrainment into the trench, which could be omitted almost entirely. [Display omitted] [ABSTRACT FROM AUTHOR]