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At least 847 records · Page 47

Automated Optically Guided System for Chemical Analysis of Single Plant and Algae Cells Using Laser Microdissection/Liquid Vortex Capture/Mass Spectrometry

Current analytical methods are not capable of providing rapid, sensitive, and comprehensive chemical analysis of a wide range of cellular constitutes of single cells (e.g., lipids, metabolites, proteins, etc.) from dispersed cell suspensions and thin tissues. This capability is important for a number of critical applications, including discovery of cellular mechanisms for coping with chemical or environmental stress and cellular response to drug treatment, to name a few. Here we introduce an optically guided platform and methodology for rapid, automated recognition, sampling, and chemical analysis of surface confined individual cells utilizing a novel hybrid laser capture microdissection/liquid vortex capture/mass spectrometry system. The system enabled automated analysis of single cells by reliably detecting and sampling them either through laser ablation from a glass microscope slide or by cutting the entire cell out of a poly(ethylene naphthalate)-coated membrane substrate that the cellular sample is deposited on. Proof of principle experiments were performed using thin tissues of Allium cepa and cultured Euglena gracilis and Phacus cell suspensions as model systems for single cell analysis using the developed method. Reliable, hands-off laser ablation sampling coupled to liquid vortex capture/mass spectrometry analysis was conducted for hundreds of individual Allium cepa cells in connected tissue. In addition, more than 300 individual Euglena gracilis and Phacus cells were analyzed automatically and sampled using laser microdissection sampling with the same liquid vortex capture/mass spectrometry analysis system. Principal component analysis-linear discriminant analysis, applied to each mass spectral dataset, was used to determine the accuracy of differentiation of the different algae cell lines.

59 BASIC BIOLOGICAL SCIENCES↗

Cell wall response of field grown Populus to Septoria infection

Due to its ability to spread quickly and result in tree mortality, Sphaerulina musiva (Septoria) is one of the most severe diseases impacting Populus . Previous studies have identified that Septoria infection induces differential expression of phenylpropanoid biosynthesis genes. However, more extensive characterization of changes to lignin in response to Septoria infection is lacking. To study the changes of lignin due to Septoria infection, four field grown, naturally variant Populus trichocarpa exhibiting visible signs of Septoria infection were sampled at health, infected, and reaction zone regions for cell wall characterization. Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and acid hydrolysis were applied to identify changes to the cell wall, and especially lignin. FTIR and subsequent principal component analysis revealed that infected and reaction zone regions were similar and could be distinguished from the non-infected (healthy) region. NMR results indicated the general trend that infected region had a higher syringyl:guaiacyl ratio and lower p -hydroxybenzoate content than the healthy regions from the same genotype. Finally, Klason lignin content in the infected and/or reaction zone regions was shown to be higher than healthy region, which is consistent with previous observations of periderm development and metabolite profiling. These results provide insights on the response of Populus wood characteristics to Septoria infection, especially between healthy and infected region within the same genotype.

59 BASIC BIOLOGICAL SCIENCES↗

The relationship between below average cognitive ability at age 5 years and the child’s experience of school at age 9

Background At age 5, while only embarking on their educational journey, substantial differences in children’s cognitive ability will already exist. The aim of this study was to examine the causal association between below average cognitive ability at age 5 years and child-reported experience of school and self-concept, and teacher-reported class engagement and emotional-behavioural function at age 9 years. Methods This longitudinal cohort study used data from 7,392 children in the Growing Up in Ireland Infant Cohort, who had completed the Picture Similarities and Naming Vocabulary subtests of the British Abilities Scales at age 5. Principal components analysis was used to produce a composite general cognitive ability score for each child. Children with a general cognitive ability score more than 1 standard deviation (SD) below the mean at age 5 were categorised as ‘Below Average Cognitive Ability’ (BACA), and those scoring above this as ‘Typical Cognitive Development’ (TCD). The outcomes of interest, measured at age 9, were child-reported experience of school, child’s self-concept, teacher-reported class engagement, and teacher-reported emotional behavioural function. Binary and multinomial logistic regression models were used to examine the association between BACA and these outcomes. Results Compared to those with TCD, those with BACA had significantly higher odds of never liking school [Adjusted odds ratio (AOR) 1.82, 95% CI 1.37–2.43, p < 0.001], of being picked on (AOR 1.27, 95% CI 1.09–1.48) and of picking on others (AOR 1.53, 95% CI 1.27–1.84). They had significantly higher odds of experiencing low self-concept (AOR 1.20, 95% CI 1.02–1.42) and emotional-behavioural difficulties (AOR 1.34, 95% CI 1.10–1.63, p = 0.003). Compared to those with TCD, children with BACA had significantly higher odds of hardly ever or never being interested, motivated and excited to learn (AOR 2.29, 95% CI 1.70–3.10). Conclusion Children with BACA at school-entry had significantly higher odds of reporting a negative school experience and low self-concept at age 9. They had significantly higher odds of having teacher-reported poor class engagement and problematic emotional-behavioural function at age 9. The findings of this study suggest BACA has a causal role in these adverse outcomes. Early childhood policy and intervention design should be cognisant of the important role of cognitive ability in school and childhood outcomes.

Bowe, Andrea K.↗

Machine learning prediction of the mechanical properties of refractory multicomponent alloys based on a dataset of phase and first principles simulation

In this work, a dataset including structural and mechanical properties of refractory multicomponent alloys was developed by fusing computations of phase diagram (CALPHAD) and density functional theory (DFT). The refractory multicomponent alloys, also named refractory complex concentrated alloys (CCAs) which contain 2–5 types of refractory elements were constructed based on Special Quasi-random Structure (SQS). The phase of alloys was predicted using CALPHAD and the mechanical property of alloys with stable and single body-centered cubic (BCC) at high temperature (over 1,500°C) was investigated using DFT-based simulation. As a result, a dataset with 393 refractory alloys and 12 features, including volume, melting temperature, density, energy, elastic constants, mechanical moduli, and hardness, were produced. To test the capability of the dataset on supporting machine learning (ML) study to investigate the property of CCAs, CALPHAD, and DFT calculations were compared with principal components analysis (PCA) technique and rule of mixture (ROM), respectively. It is demonstrated that the CALPHAD and DFT results are more in line with experimental observations for the alloy phase, structural and mechanical properties. Furthermore, the data were utilized to train a verity of ML models to predict the performance of certain CCAs with advanced mechanical properties, highlighting the usefulness of the dataset for ML technique on CCA property prediction.

36 MATERIALS SCIENCE↗

Latent-Space Dynamics for Prediction and Fault Detection in Geothermal Power Plant Operations

This paper presents a latent-space dynamic neural network (LSDNN) model for the multi-step-ahead prediction and fault detection of a geothermal power plant’s operation. The model was trained to learn the dynamics of the power generation process from multivariate time-series data and the effects of exogenous variables, such as control adjustment and ambient temperature. In the LSDNN model, an encoder–decoder architecture was designed to capture cross-correlation among different measured variables. In addition, a latent space dynamic structure was proposed to propagate the dynamics in the latent space to enable prediction. The prediction power of the LSDNN was utilized for monitoring a geothermal power plant and detecting abnormal events. The model was integrated with principal component analysis (PCA)-based process monitoring techniques to develop a fault-detection procedure. The performance of the proposed LSDNN model and fault detection approach was demonstrated using field data collected from a geothermal power plant.

15 GEOTHERMAL ENERGY↗

Chitosan Coating Incorporated with Carvacrol Improves Postharvest Guava (Psidium guajava) Quality

Guava (Psidium guajava L.) is an important economic crop grown widely in tropical and subtropical regions. Guava exhibits fast ripening and senescence as a climacteric fruit, causing a short shelf life and quality deterioration. Chitosan–essential oil nanoemulsions can be an edible coating used to improve postharvest quality attributes. In this study, chitosan was mixed with carvacrol to generate a nano-emulsoid solution containing 0.1 and 0.2% (v/v) carvacrol, using a sonic dismembrator. Guava fruit were coated with the above emulsion and postharvest quality parameters were measured during storage at 20 ± 1 °C and RH = 80 ± 5% for 8 days. The result illustrated that the particle size of the chitosan–carvacrol emulsions was nanoscale, and their high stability was demonstrated by the zeta potential and polydispersity index. Chitosan coating (2%, w/v, 310–375 kDa) containing 0.2% (v/v) carvacrol maintained postharvest quality compared to chitosan alone, with higher firmness, soluble solid content, total acid, and total phenol content, and lower weight loss and pericarp browning. The collective data were further verified by principal component analysis. A chitosan coating containing carvacrol can reduce postharvest losses. It can be applied as an effective strategy to improve postharvest fruit quality.

Agriculture↗

Neural Network Approaches for Mobile Spectroscopic Gamma-Ray Source Detection

Artificial neural networks (ANNs) for performing spectroscopic gamma-ray source identification have been previously introduced, primarily for applications in controlled laboratory settings. To understand the utility of these methods in scenarios and environments more relevant to nuclear safety and security, this work examines the use of ANNs for mobile detection, which involves highly variable gamma-ray background, low signal-to-noise ratio measurements, and low false alarm rates. Simulated data from a 2” × 4” × 16” NaI(Tl) detector are used in this work for demonstrating these concepts, and the minimum detectable activity (MDA) is used as a performance metric in assessing model performance.In addition to examining simultaneous detection and identification, binary spectral anomaly detection using autoencoders is introduced in this work, and benchmarked using detection methods based on Non-negative Matrix Factorization (NMF) and Principal Component Analysis (PCA). On average, the autoencoder provides a 12% and 23% improvement over NMF- and PCA-based detection methods, respectively. Additionally, source identification using ANNs is extended to leverage temporal dynamics by means of recurrent neural networks, and these time-dependent models outperform their time-independent counterparts by 17% for the analysis examined here. The paper concludes with a discussion on tradeoffs between the ANN-based approaches and the benchmark methods examined here.

Bilton, Kyle J. (ORCID:0000000184553689)↗

Uncovering Structure–Conductivity Relationships in Anion Exchange Membranes (AEMs) Using Interpretable Machine Learning

Anion exchange membranes (AEMs) play a vital role in the performance of water electrolyzers and fuel cells, yet their discovery and optimization remain challenging due to the complexity of structure–property relationships. In this study, we introduce a machine learning framework that leverages conditional graph neural networks (cGNNs) and descriptor-based models and a hybrid graph neural network (HGARE) to predict and interpret ionic conductivity. The descriptor-based pipeline employs principal component analysis (PCA), ablation, and SHAP analysis to identify factors governing anion conductivity, revealing electronic, topological, and compositional descriptors as key contributors. Beyond prediction, dimensionality reduction and clustering are performed by employing t-SNE and KMeans as well as SOM, which reveal distinct membranes clusters, some of which were enriched with high anion conductivity. Among graph-based approaches, the graph convolutional (GCN) achieved strong predictive performance, while the Hybrid Graph Autoencoder-Regressor Ensemble (HGARE) achieved the highest accuracy. Additionally, atom-level saliency maps from GCN provide spatial explanations for conductive behavior, revealing the importance of polarizable and flexible regions. This work contributes to the accelerated and data-driven design of high-performance AEMs.

Naghshnejad, Pegah [Department of Chemical Enginee↗

Studies of Secondary Melanoma on C57BL/6J Mouse Liver Using 1H NMR Metabolomics

NMR metabolomics, consisting of solid state high resolution (hr) magic angle spinning (MAS) 1H NMR (1H hr-MAS), liquid state high resolution 1H-NMR, and principal components analysis (PCA) has been used to study secondary metastatic B16-F10 melanoma in C57BL/6J mouse liver . The melanoma group can be differentiated from its control group by PCA analysis of the absolute concentrations or by the absolute peak intensities of metabolites from either 1H hr-MAS NMR data on intact liver tissues or liquid state 1H-NMR spectra on liver tissue extracts. In particular, we found that the absolute concentrations of alanine, glutamate, creatine, creatinine, fumarate and cholesterol are elevated in the melanoma group as compared to controls, while the absolute concentrations of succinate, glycine, glucose, and the family of linear lipids including long chain fatty acids, total choline and acylglycerol are decreased. The ratio of glycerophosphocholine to phosphocholine is increased by about 1.5 fold in the melanoma group, while the absolute concentration of total choline is actually lower in melanoma mice. These results suggest the following picture in secondary melanoma metastasis: Linear lipid levels are decreased by beta oxidation in the melanoma group, which contributes to an increase in the synthesis of cholesterol, and also provides an energy source input for TCA cycle. These findings suggest a link between lipid oxidation, the TCA cycle and the hypoxia-inducible factors (HIF) signal pathway in tumor metastases. Thus this study indicates that the metabolic profile derived from NMR analysis can provide a valuable bio-signature of malignancy and cell hypoxia in metastatic melanoma.

Environmental Molecular Sciences Laboratory↗

Coal Feed-Dependent Variation in Fly Ash Chemistry in a Single Pulverized-Combustion Unit

Four suites of fly ash, all generated at the same power plant, were selected for the study of the distribution of rare earth elements (REE). The fly ashes represented two runs of single-seam/single-mine coals and two runs of run-of-mine coals representing several coal seams from several mines. Plots of the upper continental crust-normalized REE, other parameters derived from the normalization, and the principal components analysis of the derived REE parameters (including the sum of the lanthanides plus yttrium and the ratio of the light to heavy REE) all demonstrated that the relatively rare earth-rich Fire Clay coal-derived fly ashes have a different REE distribution, with a greater concentration of REE with a relative dominance of the heavy REE, than the other fly ashes. Particularly with the Fire Clay coal-derived fly ashes, there is a systematic partitioning of the overall amount and distribution of the REE in the passage from the mechanical fly ash collection through to the last row of the electrostatic precipitator hoppers.

58 GEOSCIENCES↗

NMR Spectroscopy for Protein Higher Order Structure Similarity Assessment in Formulated Drug Products

Peptide and protein drug molecules fold into higher order structures (HOS) in formulation and these folded structures are often critical for drug efficacy and safety. Generic or biosimilar drug products (DPs) need to show similar HOS to the reference product. The solution NMR spectroscopy is a non-invasive, chemically and structurally specific analytical method that is ideal for characterizing protein therapeutics in formulation. However, only limited NMR studies have been performed directly on marketed DPs and questions remain on how to quantitively define similarity. Here, NMR spectra were collected on marketed peptide and protein DPs, including calcitonin-salmon, liraglutide, teriparatide, exenatide, insulin glargine and rituximab. The 1D 1 H spectral pattern readily revealed protein HOS heterogeneity, exchange and oligomerization in the different formulations. Principal component analysis (PCA) applied to two rituximab DPs showed consistent results with the previously demonstrated similarity metrics of Mahalanobis distance (D M ) of 3.3. The 2D 1 H- 13 C HSQC spectral comparison of insulin glargine DPs provided similarity metrics for chemical shift difference (Δδ) and methyl peak profile, i.e., 4 ppb for 1 H, 15 ppb for 13 C and 98% peaks with equivalent peak height. Finally, 2D 1 H- 15 N sofast HMQC was demonstrated as a sensitive method for comparison of small protein HOS. The application of NMR procedures and chemometric analysis on therapeutic proteins offer quantitative similarity assessments of DPs with practically achievable similarity metrics.

59 BASIC BIOLOGICAL SCIENCES↗

Predicting Short-Term Deformation in the Central Valley Using Machine Learning

Land subsidence caused by excessive groundwater pumping in Central Valley, California, is a major issue that has several negative impacts such as reduced aquifer storage and damaged infrastructures which, in turn, produce an economic loss due to the high reliance on crop production. This is why it is of utmost importance to routinely monitor and assess the surface deformation occurring. Two main goals that this paper attempts to accomplish are deformation characterization and deformation prediction. The first goal is realized through the use of Principal Component Analysis (PCA) applied to a series of Interferomtric Synthetic Aperture Radar (InSAR) images that produces eigenimages displaying the key characteristics of the subsidence. Water storage changes are also directly analyzed by the use of data from the Gravity Recovery and Climate Experiment (GRACE) twin satellites and the Global Land Data Assimilation System (GLDAS). The second goal is accomplished by building a Long Short-Term Memory (LSTM) model to predict short-term deformation after developing an InSAR time series using LiCSBAS, an open-source InSAR time series package. The model is applied to the city of Madera and produces better results than a baseline averaging model and a one dimensional convolutional neural network (CNN) based on a mean squared error metric showing the effectiveness of machine learning in deformation prediction as well as the potential for incorporation in hazard mitigation models. The model results can directly aid policy makers in determining the appropriate rate of groundwater withdrawal while maintaining the safety and well-being of the population as well as the aquifers’ integrity.

58 GEOSCIENCES↗

High-Throughput Field Plant Phenotyping: A Self-Supervised Sequential CNN Method to Segment Overlapping Plants

High-throughput plant phenotyping—the use of imaging and remote sensing to record plant growth dynamics—is becoming more widely used. The first step in this process is typically plant segmentation, which requires a well-labeled training dataset to enable accurate segmentation of overlapping plants. However, preparing such training data is both time and labor intensive. To solve this problem, we propose a plant image processing pipeline using a self-supervised sequential convolutional neural network method for in-field phenotyping systems. This first step uses plant pixels from greenhouse images to segment nonoverlapping in-field plants in an early growth stage and then applies the segmentation results from those early-stage images as training data for the separation of plants at later growth stages. The proposed pipeline is efficient and self-supervising in the sense that no human-labeled data are needed. We then combine this approach with functional principal components analysis to reveal the relationship between the growth dynamics of plants and genotypes. We show that the proposed pipeline can accurately separate the pixels of foreground plants and estimate their heights when foreground and background plants overlap and can thus be used to efficiently assess the impact of treatments and genotypes on plant growth in a field environment by computer vision techniques. This approach should be useful for answering important scientific questions in the area of high-throughput phenotyping.

59 BASIC BIOLOGICAL SCIENCES↗

Molecular distribution in the spiral arm of M51

Molecular line images of {sup 13}CO, C{sup 18}O, CN, CS, CH{sub 3}OH, and HNCO are obtained toward the spiral arm of M51 at a 7{sup ′′}×6{sup ′′} resolution with the Combined Array for Research in Millimeter-wave Astronomy. Distributions of the molecules averaged over a 300 pc scale are found to be almost similar to one another and to essentially trace the spiral arm. However, the principal component analysis shows a slight difference of distributions among molecular species, particularly for CH{sub 3}OH and HNCO. These two species do not correlate well with the star formation rate, implying that they are not enhanced by local star formation activities but by galactic-scale phenomena such as spiral shocks. Furthermore, the distributions of HNCO and CH{sub 3}OH are found to be slightly different, and their origins deserve further investigation. The present results provide us with an important clue for understanding the 300 pc scale chemical composition in the spiral arm and its relation to galactic-scale dynamics.

79 ASTRONOMY AND ASTROPHYSICS↗

ROTATION–ACTIVITY CORRELATIONS IN K AND M DWARFS. I. STELLAR PARAMETERS AND COMPILATIONS OF v sin i AND P /sin i FOR A LARGE SAMPLE OF LATE-K AND M DWARFS

The reliable determination of rotation–activity correlations (RACs) depends on precise measurements of the following stellar parameters: T {sub eff}, parallax, radius, metallicity, and rotational speed v sin i . In this paper, our goal is to focus on the determination of these parameters for a sample of K and M dwarfs. In a future paper (Paper II), we will combine our rotational data with activity data in order to construct RACs. Here, we report on a determination of effective temperatures based on the ( R – I ){sub C} color from the calibrations of Mann et al. and Kenyon and Hartmann for four samples of late-K, dM2, dM3, and dM4 stars. We also determine stellar parameters ( T {sub eff}, log( g ), and [M/H]) using the principal component analysis–based inversion technique for a sample of 105 late-K dwarfs. We compile all effective temperatures from the literature for this sample. We determine empirical radius–[M/H] correlations in our stellar samples. This allows us to propose new effective temperatures, stellar radii, and metallicities for a large sample of 612 late-K and M dwarfs. Our mean radii agree well with those of Boyajian et al. We analyze HARPS and SOPHIE spectra of 105 late-K dwarfs, and we have detected v sin i in 92 stars. In combination with our previous v sin i measurements in M and K dwarfs, we now derive P /sin i measures for a sample of 418 K and M dwarfs. We investigate the distributions of P /sin i , and we show that they are different from one spectral subtype to another at a 99.9% confidence level.

79 ASTRONOMY AND ASTROPHYSICS↗

MAGNETIC FIELD IN ATYPICAL PROMINENCE STRUCTURES: BUBBLE, TORNADO, AND ERUPTION

Spectropolarimetric observations of prominences have been obtained with the THEMIS telescope during four years of coordinated campaigns. Our aim is now to understand the conditions of the cool plasma and magnetism in “atypical” prominences, namely when the measured inclination of the magnetic field departs, to some extent, from the predominantly horizontal field found in “typical” prominences. What is the role of the magnetic field in these prominence types? Are plasma dynamics more important in these cases than the magnetic support? We focus our study on three types of “atypical” prominences (tornadoes, bubbles, and jet-like prominence eruptions) that have all been observed by THEMIS in the He i D{sub 3} line, from which the Stokes parameters can be derived. The magnetic field strength, inclination, and azimuth in each pixel are obtained by using the inversion method of principal component analysis on a model of single scattering in the presence of the Hanle effect. The magnetic field in tornadoes is found to be more or less horizontal, whereas for the eruptive prominence it is mostly vertical. We estimate a tendency toward higher values of magnetic field strength inside the bubbles than outside in the surrounding prominence. In all of the models in our database, only one magnetic field orientation is considered for each pixel. While sufficient for most of the main prominence body, this assumption appears to be oversimplified in atypical prominence structures. We should consider these observations as the result of superposition of multiple magnetic fields, possibly even with a turbulent field component.

79 ASTRONOMY AND ASTROPHYSICS↗

Evidence for the direct detection of the thermal spectrum of the non-transiting hot gas giant HD 88133 B

We target the thermal emission spectrum of the non-transiting gas giant HD 88133 b with high-resolution near-infrared spectroscopy, by treating the planet and its host star as a spectroscopic binary. For sufficiently deep summed flux observations of the star and planet across multiple epochs, it is possible to resolve the signal of the hot gas giant’s atmosphere compared to the brighter stellar spectrum, at a level consistent with the aggregate shot noise of the full data set. To do this, we first perform a principal component analysis to remove the contribution of the Earth’s atmosphere to the observed spectra. Then, we use a cross-correlation analysis to tease out the spectra of the host star and HD 88133 b to determine its orbit and identify key sources of atmospheric opacity. In total, six epochs of Keck NIRSPEC L-band observations and three epochs of Keck NIRSPEC K-band observations of the HD 88133 system were obtained. Based on an analysis of the maximum likelihood curves calculated from the multi-epoch cross-correlation of the full data set with two atmospheric models, we report the direct detection of the emission spectrum of the non-transiting exoplanet HD 88133 b and measure a radial projection of the Keplerian orbital velocity of 40 ± 15 km s{sup −1}, a true mass of 1.02{sub −0.28}{sup +0.61}M{sub J}, a nearly face-on orbital inclination of 15{sub −5}{sup +6{sup ∘}}, and an atmosphere opacity structure at high dispersion dominated by water vapor. This, combined with 11 years of radial velocity measurements of the system, provides the most up-to-date ephemeris for HD 88133.

79 ASTRONOMY AND ASTROPHYSICS↗

MAPPING THE SIMILARITIES OF SPECTRA: GLOBAL AND LOCALLY-BIASED APPROACHES TO SDSS GALAXIES

We present a novel approach to studying the diversity of galaxies. It is based on a novel spectral graph technique, that of locally-biased semi-supervised eigenvectors . Our method introduces new coordinates that summarize an entire spectrum, similar to but going well beyond the widely used Principal Component Analysis (PCA). Unlike PCA, however, this technique does not assume that the Euclidean distance between galaxy spectra is a good global measure of similarity. Instead, we relax that condition to only the most similar spectra, and we show that doing so yields more reliable results for many astronomical questions of interest. The global variant of our approach can identify very finely numerous astronomical phenomena of interest. The locally-biased variants of our basic approach enable us to explore subtle trends around a set of chosen objects. The power of the method is demonstrated in the Sloan Digital Sky Survey Main Galaxy Sample, by illustrating that the derived spectral coordinates carry an unprecedented amount of information.

79 ASTRONOMY AND ASTROPHYSICS↗