jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Marta Grzechowiak | Joanna Śliwiak | Mariusz Jaskólski | M. Ruszkowski
Source: Frontiers in Plant Science (article, 2020-06-05)
Field: Materials Science — Materials Chemistry

Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism Glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)<sup>+</sup>-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). In current perception, GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways. GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD<sup>+</sup>-specific, NAD<sup>+</sup>/NADP<sup>+</sup> dual-specific, and NADP<sup>+</sup>-specific. We determined in this work that the mitochondrial <i>At</i>GDH1 isozyme from <i>A. thaliana</i> is NAD<sup>+</sup>-specific. Altogether, <i>A. thaliana</i> expresses three GDH isozymes (<i>At</i>GDH1-3) targeted to mitochondria, of which <i>At</i>GDH2 has an extra EF-hand motif and is stimulated by calcium. Our enzymatic assays of <i>At</i>GDH1 established that its sensitivity to calcium is negligible. <i>In vivo</i> the <i>At</i>GDH1-3 enzymes form homo- and heterohexamers of varied composition. We solved the crystal structure of recombinant <i>At</i>GDH1 in the apo-form and in complex with NAD<sup>+</sup> at 2.59 and 2.03 Å resolution, respectively. We demonstrate also that both in the apo form and in 1:1 complex with NAD<sup>+</sup>, it forms <i>D</i> <sub>3</sub>-symmetric homohexamers. A subunit of <i>At</i>GDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and of domain II which binds coenzyme. Most of the subunits in our crystal structures, including those in NAD<sup>+</sup> complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the <i>At</i>GDH1-NAD<sup>+</sup> hexamer contains a serendipitous 2OG molecule in the active site, causing a dramatic (∼25°) closure of the domains. We provide convincing evidence that the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30). We also identified several MPD [(+/-)-2-methyl-2,4-pentanediol] binding sites with conserved sequence. Although <i>At</i>GDH1 is insensitive to MPD in our assays, the observation of druggable sites opens a potential for non-competitive herbicide design. NAD+ kinase ; Biochemistry ; Cofactor ; Random hexamer ; Oxidoreductase ; Biology ; Glutamate dehydrogenase ; Isozyme ; Enzyme ; Oxidative deamination ; Stereochemistry ; Chemistry ; Glutamate receptor Enzyme Structure and Function ; Amino Acid Enzymes and Metabolism ; Plant nutrient uptake and metabolism
Authors: Eugenio Meloni | Vincenzo Palma
Source: Catalysts (article, 2020-07-05)
Field: Materials Science — Materials Chemistry

Most Recent Advances in Diesel Engine Catalytic Soot Abatement: Structured Catalysts and Alternative Approaches Diesel engine emissions are typically composed of several hundred chemical compounds, partly present in the gas phase and partly in solid phase as particles, the so-called particulate matter or soot. The morphology of the catalyst is an important characteristic of soot particles’ abatement, since a good contact between catalyst and soot is mandatory. For practical purposes, the active species should be supported as a film on the structured carrier, in order to allow simultaneous soot filtration and combustion. This review focuses on the most recent advances in the development of structured catalysts for diesel engine catalytic soot combustion, characterized by different active species and supports, as well as by different geometric configurations (monoliths, foams, ceramic papers, or wire mesh); the most important peculiar properties are highlighted and summarized. Moreover, a critical review of the most recent advances in modeling studies is also presented in this paper. In addition, some highlights on some of the most recent alternative approaches proposed for limiting the soot emissions from diesel engines have been given, delineating feasible alternatives to the classical strategies nowadays used. Soot ; Diesel exhaust ; Combustion ; Diesel fuel ; Diesel particulate filter ; Diesel engine ; Particulates ; Limiting ; Environmental science ; Process engineering ; Materials science ; Waste management ; Chemistry ; Mechanical engineering ; Engineering ; Automotive engineering Catalytic Processes in Materials Science ; Catalysis and Oxidation Reactions ; Advanced Combustion Engine Technologies
Authors: Liangsong Huang | Xitao Lv | Yongzhe Tang | Guanghui Ge | Peng Zhang | Yuxia Li
Source: Polymers (article, 2020-09-17)
Field: Materials Science — Materials Chemistry

Effect of Alumina Nanowires on the Thermal Conductivity and Electrical Performance of Epoxy Composites Alumina nanowires (Al<sub>2</sub>O<sub>3</sub>-NWs)/epoxy resin composites have been thoroughly studied due to their excellent insulating and dielectric performance. In particular, understanding the effect of nano-alumina with different morphologies on the dielectric performance of composites is of great significance. In this study, Al<sub>2</sub>O<sub>3</sub>-NWs with lengths of approximately 100 nm and diameters of approximately 5 nm were prepared and blended with anepoxy resin to form composites, and the effect of the mass fraction of fillers on the thermal conductivity of the composites was investigated. Specifically, the effect of alumina fillers with ananowire structure on the insulating and dielectric performance and breakdown strength of the epoxy composites were analyzed. The influence principle of the interfacial effect and heat accumulation on the dielectric and insulating properties of the composites were described. The results demonstrated that the thermal conductivity of Al<sub>2</sub>O<sub>3</sub>-NWs/epoxy resin composites was higher than that of the bare epoxy resin. The thermal conductivity of Al<sub>2</sub>O<sub>3</sub>-NWs/epoxy resin composites increased with increasing mass fraction of fillers. When the mass fraction of fillers was 10%, the thermal conductivity of the composite was 134% higher than that of the epoxy resin matrix. The volume resistivity of the composites first increased and then decreased as the mass fraction of fillers increased, while the dielectric constant of the composites increased with increasing mass fraction of fillers and decreasing frequency. The dielectric loss of the composites decreased and then increased as the mass fraction of fillers increased, and it increased with increasing frequency. Additionally, the alternating current breakdown strength of the composites first increased and then decreased withincreasingmass fraction of fillers. Materials science ; Epoxy ; Composite material ; Dielectric ; Mass fraction ; Thermal conductivity ; Volume fraction ; Composite number ; Electrical resistivity and conductivity ; Conductivity ; Dielectric loss ; Nanowire High voltage insulation and dielectric phenomena ; Dielectric materials and actuators ; Electromagnetic wave absorption materials
Authors: Pratik Shah | Riddhi Nagda | Il Lae Jung | Yong Joo Bhang | Sang‐Woo Jeon | Chang Seop Lee | Changwoo Do | Keonwook Nam | Young Min Kim | Sooyeon Park | Young Hoon Roh | Peter W. Thulstrup | Morten J. Bjerrum | Tae‐Hwan Kim | Seong Wook Yang
Source: ACS Nano (article, 2020-06-11)
Field: Materials Science — Materials Chemistry

Noncanonical Head-to-Head Hairpin DNA Dimerization Is Essential for the Synthesis of Orange Emissive Silver Nanoclusters DNA secondary structures, such as dimers and hairpins, are important for the synthesis of DNA template-embedded silver nanoclusters (DNA/AgNCs). However, the arrangement of AgNCs within a given DNA template and how the AgNC influences the secondary structure of the DNA template are still unclear. Here, we introduce a noncanonical head-to-head hairpin DNA nanostructure that is driven by orange-emissive AgNCs. Through detailed in-gel analysis, sugar backbone switching, inductively coupled plasma mass spectrometry, small-angle X-ray scattering, and small angle neutron scattering, we show that the orange-emissive AgNCs mediate cytosine-Ag-cytosine bridging between two six-cytosine loop (6C-loop) hairpin DNA templates. Unlike green, red, or far-red emissive AgNCs, which are embedded inside a hairpin and duplex DNA template, the orange-emissive AgNCs are localized on the interface between the two 6C-loop hairpin DNA templates, thereby linking them. Moreover, we found that deoxyribose in the backbone of the 6C-loop at the third and fourth cytosines is crucial for the formation of the orange-emissive AgNCs and the head-to-head hairpin DNA structure. Taken together, we suggest that the specific wavelength of AgNCs fluorescence is determined by the mutual interaction between the secondary or tertiary structures of DNA- and AgNC-mediated intermolecular DNA cross-linking. Nanoclusters ; DNA ; Cytosine ; Chemistry ; Materials science ; Crystallography ; Biophysics ; Nanotechnology ; Biochemistry ; Biology Nanocluster Synthesis and Applications ; Gold and Silver Nanoparticles Synthesis and Applications ; Advanced biosensing and bioanalysis techniques
Authors: Zhezhe Han | Jian Li | Biao Zhang | Md. Moinul Hossain | Chuanlong Xu
Source: Fuel (article, 2020-11-29)
Field: Chemistry — Analytical Chemistry

Prediction of combustion state through a semi-supervised learning model and flame imaging Artificial intelligence ; Computer science ; Artificial neural network ; Combustion ; Machine learning ; Pattern recognition (psychology) ; Autoencoder ; Robustness (evolution) ; Classifier (UML) Spectroscopy and Chemometric Analyses ; Thermography and Photoacoustic Techniques ; Combustion and flame dynamics
Authors: Wiebke Kämper | Stephen J. Trueman | Iman Tahmasbian | Shahla Hosseini Bai
Source: Remote Sensing (article, 2020-10-17)
Field: Chemistry — Analytical Chemistry

Rapid Determination of Nutrient Concentrations in Hass Avocado Fruit by Vis/NIR Hyperspectral Imaging of Flesh or Skin Fatty acid composition and mineral nutrient concentrations can affect the nutritional and postharvest properties of fruit and so assessing the chemistry of fresh produce is important for guaranteeing consistent quality throughout the value chain. Current laboratory methods for assessing fruit quality are time-consuming and often destructive. Non-destructive technologies are emerging that predict fruit quality and can minimise postharvest losses, but it may be difficult to develop such technologies for fruit with thick skin. This study aimed to develop laboratory-based hyperspectral imaging methods (400–1000 nm) for predicting proportions of six fatty acids, ratios of saturated and unsaturated fatty acids, and the concentrations of 14 mineral nutrients in Hass avocado fruit from 219 flesh and 194 skin images. Partial least squares regression (PLSR) models predicted the ratio of unsaturated to saturated fatty acids in avocado fruit from both flesh images (R2 = 0.79, ratio of prediction to deviation (RPD) = 2.06) and skin images (R2 = 0.62, RPD = 1.48). The best-fit models predicted parameters that affect postharvest processing such as the ratio of oleic:linoleic acid from flesh images (R2 = 0.67, RPD = 1.63) and the concentrations of boron (B) and calcium (Ca) from flesh images (B: R2 = 0.61, RPD = 1.51; Ca: R2 = 0.53, RPD = 1.71) and skin images (B: R2 = 0.60, RPD = 1.55; Ca: R2 = 0.68, RPD = 1.57). Many quality parameters predicted from flesh images could also be predicted from skin images. Hyperspectral imaging represents a promising tool to reduce postharvest losses of avocado fruit by determining internal fruit quality of individual fruit quickly from flesh or skin images. Flesh ; Postharvest ; Partial least squares regression ; Nutrient ; Linoleic acid ; Horticulture ; Food science ; Fatty acid ; Chemistry ; Botany ; Biology ; Mathematics ; Biochemistry Spectroscopy and Chemometric Analyses ; Date Palm Research Studies ; Postharvest Quality and Shelf Life Management
Authors: Angela R. Possinger | Scott W. Bailey | Thiago Massao Inagaki | Ingrid Kögel‐Knabner | James J. Dynes | Zachary A. Arthur | Johannes Lehmann
Source: Geoderma (article, 2020-06-08)
Field: Materials Science — Biomaterials

Organo-mineral interactions and soil carbon mineralizability with variable saturation cycle frequency Soil water ; Saturation (graph theory) ; Chemistry ; Environmental chemistry ; Soil science ; Dissolution ; Mineralization (soil science) ; Soil carbon ; Organic matter ; Cycling ; Total organic carbon ; Mineralogy ; Environmental science Clay minerals and soil interactions ; Geochemistry and Geologic Mapping ; Heavy metals in environment
Authors: Chao Li | Bin Li | Dapeng Ye
Source: IEEE Access (article, 2020-01-01)
Field: Chemistry — Analytical Chemistry

Analysis and Identification of Rice Adulteration Using Terahertz Spectroscopy and Pattern Recognition Algorithms Rice adulteration is a severe problem in agro-products and food regulatory agencies, suppliers, and consumers. In this study, to effectively distinguish whether high-quality rice is mixed with low-quality rice, detection and analysis of adulterated rice in five levels with different mixing proportions was conducted via terahertz spectroscopy and pattern recognition algorithms. Initially, samples were prepared and spectral data were acquired by using the terahertz transmission mode, and a principal component analysis (PCA) algorithm was applied to extract features from original spectrum information and reduce data dimensions. Subsequently, partial least squares-discriminant analysis (PLS-DA), support vector machine (SVM), and a back propagation neural network (BPNN) combined with the absorption spectra after different pretreatments, including standard normal variate (SNV) transformation, baseline correction (BC), and first derivative (1st derivative), were applied to establish the classification models. Results indicate that an SVM model employing the absorption spectra with a 1st derivative pretreatment exhibits the best discrimination ability, with an accuracy up to 97.33% in the prediction set. This result proves that terahertz spectroscopy combined with chemometric methods can be an effective tool to identify rice adulteration levels. Principal component analysis ; Linear discriminant analysis ; Terahertz spectroscopy and technology ; Pattern recognition (psychology) ; Terahertz radiation ; Artificial intelligence ; Support vector machine ; Computer science ; Algorithm ; Mathematics ; Materials science Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Identification and Quantification in Food
Authors: Agus Arip Munawar | Yuswar Yunus | Devianti Devianti | Purwana Satriyo
Source: Data in Brief (article, 2020-04-08)
Field: Chemistry — Analytical Chemistry

Calibration models database of near infrared spectroscopy to predict agricultural soil fertility properties Presented paper describes spectroscopic dataset and calibration models database of near infrared spectroscopy (NIRS) used to predict agricultural soil fertility properties. Near infrared spectra data in form of absorbance spectrum were acquired in wavelength range from 1000 to 2500 nm for a total of 40 bulk soil samples amounted of 10 g per each bulk. Soil fertility properties, presented as soil nitrogen (N), phosphorus (P). potassium (K), soil pH, magnesium (Mg) and calcium (Ca), were measured by means of wet chemical analysis. Calibration models, used to predict those soil fertility parameters were developed using two different regression algorithms namely principal component regression (PCR) and partial least square regression (PLSR) respectively. Prediction performance can be evaluated and justified by looking their statistical indicators: correlation of determination (R<sup>2</sup>), correlation coefficient (r), root mean square error (RMSE) and residual predictive deviation (RPD). Spectra data can also be corrected in order to improve and enhance prediction performance. Obtained NIRS dataset and models database can be used as a rapid and simultaneous method to determine agricultural soil fertility properties. Principal component regression ; Soil fertility ; Soil test ; Coefficient of determination ; Partial least squares regression ; Calibration ; Mean squared error ; Correlation coefficient ; Principal component analysis ; Residual ; Environmental science ; Near-infrared spectroscopy ; Regression analysis ; Linear regression ; Mathematics ; Soil science ; Statistics ; Soil water ; Algorithm Spectroscopy and Chemometric Analyses ; Soil Geostatistics and Mapping ; Mineral Processing and Grinding
Authors: Xiu Jin | Shaowen Li | Zhang Wu | Juanjuan Zhu | Jia Sun
Source: Applied Sciences (article, 2020-02-23)
Field: Chemistry — Analytical Chemistry

Prediction of Soil-Available Potassium Content with Visible Near-Infrared Ray Spectroscopy of Different Pretreatment Transformations by the Boosting Algorithms The application of visible near-infrared (VIS-NIR) analysis technology to quantify the nutrients in soil has been widely recognized. It is important to improve the performance of regression models that can predict the soil-available potassium concentration. This study collected soil samples from southern Anhui, China, and concentrated on the modelling methods by using 29 pretreatment methods. The results show that a combination of three methods, Savitzky–Golay, standard normal variate, and dislodge tendency, exhibited better stability than others because it was the most capable of achieving levels A and B of the ratio of performance of deviation. The boosting algorithms that form an ensemble of multiple weak predictors exhibited better performance than partial least square (PLS) regression and support vector regression (SVR) for the prediction of soil-available potassium. These regression models could be employed to precisely predict the soil-available potassium concentration. Boosting (machine learning) ; Partial least squares regression ; Potassium ; Support vector machine ; Soil test ; Regression ; Regression analysis ; Mathematics ; Soil science ; Environmental science ; Algorithm ; Chemistry ; Computer science ; Soil water ; Statistics ; Artificial intelligence Spectroscopy and Chemometric Analyses ; Soil Geostatistics and Mapping ; Geochemistry and Geologic Mapping
Authors: Zhiming Zhang | Chenghan Ding | Yuan Li | Hanzhong Ke | Guoe Cheng
Source: SN Applied Sciences (article, 2020-03-16)
Field: Chemistry — Inorganic Chemistry

Efficient removal of tetracycline hydrochloride from aqueous solution by mesoporous cage MOF-818 Adsorption ; Aqueous solution ; Endothermic process ; Chemistry ; Langmuir ; Mesoporous material ; Langmuir adsorption model ; Freundlich equation ; Chemisorption ; Chemical engineering ; Inorganic chemistry ; Nuclear chemistry ; Physical chemistry ; Organic chemistry ; Catalysis Metal-Organic Frameworks: Synthesis and Applications ; Covalent Organic Framework Applications ; Adsorption and biosorption for pollutant removal
Authors: Wei Zhong | Ji‐Cheng Zhao
Source: Acta Materialia (article, 2020-10-01)
Field: Materials Science — Biomaterials

A comprehensive diffusion mobility database comprising 23 elements for magnesium alloys Materials science ; Diffusion ; Reliability (semiconductor) ; Alloy ; Activation energy ; Database ; Thermodynamics ; Computer science ; Physical chemistry ; Metallurgy ; Chemistry ; Physics Magnesium Alloys: Properties and Applications ; Aluminum Alloys Composites Properties ; Hydrogen Storage and Materials
Authors: Jia Tang | Haihong Shi | Guanyu Ma | Liangping Luo | Zhenghua Tang
Source: Frontiers in Bioengineering and Biotechnology (review, 2020-10-08)
Field: Materials Science — Materials Chemistry

Ultrasmall Au and Ag Nanoclusters for Biomedical Applications: A Review Noble metal (e.g., Au, Ag, Pt, Pd, and their alloys) nanoclusters (NCs) have emerged as a new type of functional nanomaterial in nanoscience and nanotechnology. Owing to their unique properties, such as their ultrasmall dimension, enhanced photoluminescence, low toxicity, and excellent biocompatibility, noble metal NCs-especially Au and Ag NCs-have found various applications in biomedical regimes. This review summarizes the recent advances made in employing ultrasmall Au and Ag NCs for biomedical applications, with particular emphasis on bioimaging and biosensing, anti-microbial applications, and tumor targeting and cancer treatment. Challenges, including the shared and specific challenges for Au and Ag NC toward biomedical applications, and future directions are briefly discussed at the end. Nanoclusters ; Nanotechnology ; Materials science Nanocluster Synthesis and Applications ; Gold and Silver Nanoparticles Synthesis and Applications ; Advanced Nanomaterials in Catalysis
Authors: Emma Danelius | Steve Halaby | Wilfred A. van der Donk | Tamir Gonen
Source: Natural Product Reports (review, 2020-09-17)
Field: Materials Science — Materials Chemistry

MicroED in natural product and small molecule research Covering: 2013 to 2020The electron cryo-microscopy (cryo-EM) method Microcrystal Electron Diffraction (MicroED) allows the collection of high-resolution structural data from vanishingly small crystals that appear like amorphous powders or very fine needles. Since its debut in 2013, data collection and analysis schemes have been fine-tuned, and there are currently close to 100 structures determined by MicroED. Although originally developed to study proteins, MicroED is also very powerful for smaller systems, with some recent and very promising examples from the field of natural products. Herein, we review what has been achieved so far and provide examples of natural product structures, as well as demonstrate the expected future impact of MicroED to the field of natural product and small molecule research. Cryo-electron microscopy ; Electron microscope ; Amorphous solid ; Nanotechnology ; Materials science ; Resolution (logic) ; Diffraction ; Electron diffraction ; Product (mathematics) ; High resolution ; Crystallography ; Chemistry ; Physics ; Optics ; Computer science ; Nuclear magnetic resonance ; Geology Enzyme Structure and Function ; Microbial Natural Products and Biosynthesis ; Bioactive Compounds and Antitumor Agents
Authors: Partha Pratim Bag | Govind Singh | Shuvendu Singha | Gourisankar Roymahapatra
Source: Engineered Science (review, 2020-01-01)
Field: Chemistry — Inorganic Chemistry

Synthesis of Metal-Organic Frameworks (MOFs) and Their Applications to Biology, Catalysis and Electrochemical Charge Storage: A Mini Review Metal-organic framework ; Nanotechnology ; Electrochemistry ; Materials science ; Charge (physics) ; Electrochemical energy storage ; Chemistry ; Supercapacitor ; Organic chemistry ; Electrode ; Physics ; Physical chemistry Metal-Organic Frameworks: Synthesis and Applications ; Advanced Nanomaterials in Catalysis ; Machine Learning in Materials Science