jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Youngwoo Lee | Thomas W. Okita | Daniel B. Szymanski
Source: The Plant Cell (article, 2021-07-14)
Field: Materials Science — Materials Chemistry

A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone Multiprotein complexes execute and coordinate diverse cellular processes such as organelle biogenesis, vesicle trafficking, cell signaling, and metabolism. Knowledge about their composition and localization provides useful clues about the mechanisms of cellular homeostasis and system-level control. This is of great biological importance and practical significance in heterotrophic rice (Oryza sativa) endosperm and aleurone-subaleurone tissues, which are a primary source of seed vitamins and stored energy. Dozens of protein complexes have been implicated in the synthesis, transport, and storage of seed proteins, lipids, vitamins, and minerals. Mutations in protein complexes that control RNA transport result in aberrant endosperm with shrunken and floury phenotypes, significantly reducing seed yield and quality. The purpose of this study was to broadly predict protein complex composition in the aleurone-subaleurone layers of developing rice seeds using co-fractionation mass spectrometry. Following orthogonal chromatographic separations of biological replicates, thousands of protein elution profiles were subjected to distance-based clustering to enable large-scale multimerization state measurements and protein complex predictions. The predicted complexes had predicted functions across diverse functional categories, including novel heteromeric RNA binding protein complexes that may influence seed quality. This effective and open-ended proteomics pipeline provides useful clues about system-level posttranslational control during the early stages of rice seed development. Endosperm ; Aleurone ; Biology ; Proteomics ; Biochemistry ; Proteome ; Endomembrane system ; Oryza sativa ; Biogenesis ; Cell biology ; Cell ; Golgi apparatus ; Gene Enzyme Structure and Function ; Photosynthetic Processes and Mechanisms ; Plant nutrient uptake and metabolism
Authors: Maik Pietzner | Eleanor Wheeler | Julia Carrasco-Zanini | Nicola D. Kerrison | Erin Oerton | Mine Koprulu | Jian’an Luan | Aroon D. Hingorani | Steve A. Williams | Nicholas J. Wareham | Claudia Langenberg
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-03-19)
Field: Chemistry — Spectroscopy

Cross-platform proteomics to advance genetic prioritisation strategies ABSTRACT Discovery of protein quantitative trait loci (pQTLs) has been enabled by affinity-based proteomic techniques and is increasingly used to guide genetically informed drug target evaluation. Large-scale proteomic data are now being created, but systematic, bidirectional assessment of platform differences is lacking, restricting clinical translation. We compared genetic, technical, and phenotypic determinants of 871 protein targets measured using both aptamer-(SomaScan® Platform v4) and antibody-based (Olink) assays in up to 10,708 individuals. Correlations coefficients for overlapping protein targets varied widely (median 0.38, IQR: 0.08-0.64). We found that 64% of pQTLs were shared across both platforms among all identified 608 cis - and 1,315 trans -pQTLs with sufficient power for replication, but with correlations of effect estimates being lower than previously reported ( cis : 0.41, trans : 0.34). We identified technical, protein, and variant characteristics that contributed significantly to platform differences and found contradicting phenotypic associations attributable to those. We demonstrate how integrating phenomic and gene expression data improves genetic prioritisation strategies, including platform-specific pQTLs. Computational biology ; Biology ; Proteomics ; Quantitative trait locus ; Phenotype ; Trait ; Replication (statistics) ; Protein expression ; Gene ; Genetics ; Bioinformatics ; Computer science Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Genetic Associations and Epidemiology
Authors: Jian Zhao | Jun Chen
Source: Horticulturae (article, 2021-05-11)
Field: Chemistry — Analytical Chemistry

Detecting Maturity in Fresh Lycium barbarum L. Fruit Using Color Information The accurate quantitative maturity detection of fresh Lycium barbarum L. (L. barbarum) fruit is the key to determine whether fruit are suitable for harvesting or not and can also be helpful to improve the quality of post-harvest processing. To achieve this goal, abnormal samples were eliminated by the Mahalanobis Distance (MD), and nine components (i.e., R, G, B, H, S, V, L, a, and b) of the ripe fruit, half-ripe fruit, and unripe fruit were extracted, firstly. Then, significant component combinations of the three fruits beneficial to the extraction of their areas were determined. Through binary processing, morphology processing, and other image processing methods, a quantitative maturity detection model of fruit was established based on the support vector machine (SVM) model. On this basis, field experiments were conducted to verify and compare the relationship between the prediction results of the model and the picking forces of fruit. Field experiments showed that the accuracies of both the training set and prediction set were 100% and the prediction results of the model were consistent with the picking forces of fruit. Findings provided a theoretical basis for the accurate quantitative maturity detection of fresh L. barbarum fruit. Lycium ; Support vector machine ; Mahalanobis distance ; Horticulture ; Maturity (psychological) ; Mathematics ; Artificial intelligence ; Botany ; Pattern recognition (psychology) ; Computer science ; Biology Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI ; Leaf Properties and Growth Measurement
Authors: Didier Fraix‐Burnet | Charles Bouveyron | J. Moultaka
Source: Astronomy and Astrophysics (article, 2021-03-06)
Field: Chemistry — Analytical Chemistry

Unsupervised classification of SDSS galaxy spectra Context. Defining templates of galaxy spectra is useful to quickly characterise new observations and organise databases from surveys. These templates are usually built from a pre-defined classification based on other criteria. Aims. We present an unsupervised classification of 702 248 spectra of galaxies and quasars with redshifts smaller than 0.25 that were retrieved from the Sloan Digital Sky Survey (SDSS) database, release 7. Methods. The spectra were first corrected for redshift, then wavelet-filtered to reduce the noise, and finally binned to obtain about 1437 wavelengths per spectrum. The unsupervised clustering algorithm Fisher-EM, relying on a discriminative latent mixture model, was applied on these corrected spectra. The full set and several subsets of 100 000 and 300 000 spectra were analysed. Results. The optimum number of classes given by a penalised likelihood criterion is 86 classes, of which the 37 most populated gather 99% of the sample. These classes are established from a subset of 302 214 spectra. Using several cross-validation techniques we find that this classification agrees with the results obtained on the other subsets with an average misclassification error of about 15%. The large number of very small classes tends to increase this error rate. In this paper, we do an initial quick comparison of our classes with literature templates. Conclusions. This is the first time that an automatic, objective and robust unsupervised classification is established on such a large number of galaxy spectra. The mean spectra of the classes can be used as templates for a large majority of galaxies in our Universe. Galaxy ; Pattern recognition (psychology) ; Cluster analysis ; Computer science ; Spectral line ; Discriminative model ; Redshift ; Artificial intelligence ; Astrophysics ; Wavelet ; Physics ; Mathematics ; Astronomy Spectroscopy and Chemometric Analyses ; Blind Source Separation Techniques ; Bayesian Methods and Mixture Models
Authors: Yu. V. Zaika | Ekaterina K. Kostikova | Yu. S. Nechaev
Source: Technical Physics (article, 2021-02-01)
Field: Materials Science — Materials Chemistry

Peaks of Hydrogen Thermal Desorption: Simulation and Interpretation Different models of hydrogen thermal desorption peaks have been analyzed. The model of volume-averaged concentration dynamics with a continuum parameter makes it possible to integrally take into consideration the dominance of limiting factors: diffusion and recombination of atoms into desorbing molecules. An analytical symmetry criterion for peaks versus the method of expanding a composed spectrum into a series of Gaussian curves is suggested. Modifications of (i) the Kissinger method to estimate the activation energy of desorption in experiments with several material heating rates and (ii) a procedure for solving the inverse problem of unimodal peak parametrical identification from one heat rate are presented. Comparison with the diffusion model with dynamic boundary conditions has been carried out. It has been shown that local peaks may arise not only because of release of hydrogen atoms with different binding energies captured by volume traps, but also because of interaction between volume and surface processes and heat-induced surface structure modifications. The parameters of deuterium thermal desorption from ISO-880U graphite have been estimated. Desorption ; Thermal desorption ; Deuterium ; Thermodynamics ; Materials science ; Hydrogen ; Thermal ; Volume (thermodynamics) ; Diffusion ; Graphite ; Chemical physics ; Atomic physics ; Molecular physics ; Physics ; Physical chemistry ; Chemistry ; Adsorption Nuclear Materials and Properties ; Thermal and Kinetic Analysis ; Nuclear Physics and Applications
Authors: Qiang Qi | Mingzhong Zhao | Fei Sun | Yingchun Zhang | Shouxi Gu | Baolong Ji | Hai-Shan Zhou | Yasuhisa Oya | Songlin Liu | Guang–Nan Luo
Source: Nuclear Materials and Energy (article, 2021-06-08)
Field: Materials Science — Materials Chemistry

Investigation on effects of tritium release behavior in Li4SiO4 pebbles For deuterium–tritium fusion reactor, the fuel of tritium is not available naturally. Tritium should be produced by the reaction of Li (n, ɑ) T. Li4SiO4 is one of promising candidates due to its high lithium density. In present work, effects of tritium release behavior from Li4SiO4 have been investigated and compared. The main release peak at lower temperature was attributed to tritium located on/near the grain surface and chemical adsorption on pore surface. The small peak at higher temperature was designated as tritium diffusion from grain including lattice and boundary. The tritium release behavior was simulated by diffusion model and surface reaction model. Tritium behavior is controlled by both diffusion and surface reaction for different stages. Based on the desorption theory, the kinetic parameters were obtained. The effects on tritium release behavior were studied. The porosity has significant effects on tritium release. Higher porosity has large specific surface providing more activation sites and fast channels for tritium release which results in lower temperature of tritium release. The main tritium release form was considered as tritium water. The release peak of deuterium moved towards lower temperature after adsorbing water vapor for 1800 h. It was demonstrated that adsorbing water was beneficial for tritium release due to isotope exchange. Compared the effects of porosity and water vapor, higher porosity has larger effects on tritium release in the present work. Based on the work, the tritium release is controlled by both diffusion and surface reaction at different stage and affected by comprehensive effects including porosity and adsorption water. Tritium ; Deuterium ; Porosity ; Diffusion ; Chemistry ; Radiochemistry ; Adsorption ; Tritiated water ; Heavy water ; Fusion power ; Water vapor ; Materials science ; Nuclear physics ; Plasma ; Thermodynamics ; Physical chemistry Fusion materials and technologies ; Muon and positron interactions and applications ; Nuclear Materials and Properties
Authors: Patrizia Andreozzi | Cristina Simó | Paolo Moretti | Joaquín Martínez Porcel | Tanja Ursula Lüdtke | María de los Ángeles Ramírez | Lorenza Tamberi | Marco Marradi | Heinz Amenitsch | Jordi Llop | María Grazia Ortore | Sergio Moya
Source: Small (article, 2021-07-18)
Field: Materials Science — Biomaterials

Novel Core–Shell Polyamine Phosphate Nanoparticles Self‐Assembled from PEGylated Poly(allylamine hydrochloride) with Low Toxicity and Increased In Vivo Circulation Time An approach for reducing toxicity and enhancing therapeutic potential of supramolecular polyamine phosphate nanoparticles (PANs) through PEGylation of polyamines before their assembly into nanoparticles is presented here. It is shown that the number of polyethylene glycol (PEG) chains for polyamine largely influence physico-chemical properties of PANs and their biological endpoints. Poly(allylamine hydrochloride) (PAH) are functionalized through carbodiimide chemistry with three ratios of PEG molecules per PAH chain: 0.1, 1, and 10. PEGylated PAH is then assembled into PANs by exposing the polymer to phosphate buffer solution. PANs decrease size and surface charge with increasing PEG ratios as evidenced by dynamic light scattering and zeta potential measurements, with the ten PEG/PAH ratio PANs having practically zero charge. Small angle X-ray scattering (SAXS) proves that PEG chains form a shell around a polyamine core, which is responsible for the screening of positive charges. MTT experiments show that the screening of amine groups decreases nanoparticle toxicity, with the lowest toxicity for the 10 PEG/PAH ratio. Fluorescence correlation spectroscopy (FCS) proves less interaction with proteins for PEGylated PANs. Positron emission tomography (PET) imaging of <sup>18</sup> F labelled PANs shows longer circulation time in healthy mice for PEGylated PANs than non-PEGylated ones. PEGylation ; PEG ratio ; Allylamine ; Dynamic light scattering ; Polyethylene glycol ; Chemistry ; Zeta potential ; Nanoparticle ; Nuclear chemistry ; Polyelectrolyte ; Materials science ; Organic chemistry ; Polymer ; Nanotechnology Nanoparticle-Based Drug Delivery ; Polymer Surface Interaction Studies ; Graphene and Nanomaterials Applications
Authors: Peng‐Kai Kao | Bryan VanSaders | Sharon C. Glotzer | Michael J. Solomon
Source: Scientific Reports (article, 2021-05-26)
Field: Materials Science — Materials Chemistry

Accelerated annealing of colloidal crystal monolayers by means of cyclically applied electric fields External fields are commonly applied to accelerate colloidal crystallization; however, accelerated self-assembly kinetics can negatively impact the quality of crystal structures. We show that cyclically applied electric fields can produce high quality colloidal crystals by annealing local disorder. We find that the optimal off-duration for maximum annealing is approximately one-half of the characteristic melting half lifetime of the crystalline phase. Local six-fold bond orientational order grows more rapidly than global scattering peaks, indicating that local restructuring leads global annealing. Molecular dynamics simulations of cyclically activated systems show that the ratio of optimal off-duration for maximum annealing and crystal melting time is insensitive to particle interaction details. This research provides a quantitative relationship describing how the cyclic application of fields produces high quality colloidal crystals by cycling at the fundamental time scale for local defect rearrangements; such understanding of dynamics and kinetics can be applied for reconfigurable colloidal assembly. Annealing (glass) ; Crystallization ; Materials science ; Colloidal crystal ; Chemical physics ; Colloid ; Scattering ; Electric field ; Molecular dynamics ; Kinetics ; Monolayer ; Simulated annealing ; Crystal (programming language) ; Crystallography ; Nanotechnology ; Chemistry ; Thermodynamics ; Optics ; Physics ; Composite material ; Computer science ; Physical chemistry ; Computational chemistry ; Classical mechanics Pickering emulsions and particle stabilization ; Material Dynamics and Properties ; Electrostatics and Colloid Interactions
Authors: GRIGORIA-KALLIOPI MARIOLI-SAPSAKOU | Malamati Kourti
Source: Anticancer Research (review, 2021-11-30)
Field: Chemistry — Organic Chemistry

Targeting Production of Reactive Oxygen Species as an Anticancer Strategy Cancer remains the second leading cause of death worldwide. Research is currently focused on finding novel anticancer therapies and elucidating their mechanisms of action. Cellular redox balance is a promising target for new therapies, as cancer cells already have elevated levels of oxidizing agents due to hypermetabolism and genetic instability. Although free radicals are actively involved in vital cellular signaling pathways, they have also been implicated in certain diseases, including cancer. The aim of this review was to highlight the involvement of oxidative stress in the mechanism of action of anticancer agents. The difference in cellular redox balance between normal and cancer cells is discussed as a potential anticancer target, along with various examples of approved or experimental drugs that may alter the redox state. These drugs are presented in relation to their pro-oxidant or antioxidant mechanisms, with the consequent goal of underscoring the importance of such mechanisms in the overall efficacy of anticancer drugs. Oxidative stress ; Reactive oxygen species ; Cancer ; Cancer cell ; Mechanism of action ; Detoxification (alternative medicine) ; Pharmacology ; Mechanism (biology) ; Medicine ; Bioinformatics ; Biology ; Cancer research ; Cell biology ; Biochemistry ; Internal medicine ; In vitro ; Pathology Free Radicals and Antioxidants ; Glutathione Transferases and Polymorphisms ; Metal complexes synthesis and properties
Authors: Nikita Naidu | Kamlesh Wadher | Milind Umekar
Source: Journal of Drug Delivery and Therapeutics (article, 2021-02-15)
Field: Materials Science — Biomaterials

An Overview on Biomaterials: Pharmaceutical and Biomedical Applications The development of biomaterials have existed from around half a century and manifest its use in different fields. Biomaterials are used in living creature body, looking on its biocompatibility nature. In recent years, advances of biomaterials are showing a marked presence in the fast growing fields of pharmaceuticals and medicines. According to their availability, different types of biomaterials like metal, ceramic, polymer and their composites are used for several purpose in the body. In this review article, types of biomaterials have been discussed with their advantages, disadvantages and recent applications in the pharmaceutical field such as implants used to mimic the structure and function of tissues, dental implants, wound healing, cell regeneration, regenerative medicines, delivery of drugs and different organ regeneration. Organ regeneration leading to replacement of organs such as heart, trachea and lungs etc. by use of specific biomaterials have been reported with the diagnosis of diseases and its treatment. Regeneration (biology) ; Regenerative medicine ; Biocompatibility ; Tissue engineering ; Biocompatible material ; Biomedical engineering ; Nanotechnology ; Medicine ; Materials science ; Stem cell ; Biology ; Cell biology Electrospun Nanofibers in Biomedical Applications ; 3D Printing in Biomedical Research ; Bone Tissue Engineering Materials
Authors: Rubing Wang | Shuang‐Gang Ma | Cooper S. Jamieson | Rong‐Mei Gao | Yun‐Bao Liu | Yong Li | Xiaojing Wang | Yuhuan Li | K. N. Houk | Jing Qu | Shi‐Shan Yu
Source: Chemical Science (article, 2021-01-01)
Field: Chemistry — Organic Chemistry

Library construction of stereochemically diverse isomers of spirooliganin: their total synthesis and antiviral activity The construction of libraries of stereoisomers of natural products serves as an important approach to investigating the correlation between the stereostructure and biological activity. However, the total synthesis and isomerzation of polycyclic scaffolds with multiple chrial centers are rare. Spirooliganin (<b>1</b>), a new skeleton natural product isolated from the plant <i>Illicium oligandrum</i>, was structurally characterized by comprehensive analysis of NMR spectroscopic data and ECD which revealed an unprecedented 5-6-6-6-7 polycyclic framework with six chiral centers. Here we report a 17-step total synthesis to prepare a library of stereochemically diverse isomers of spirooliganin, including 16 diastereoisomers and 16 regioisomers. In addition to a regioselective hetero-Diels-Alder cycloaddition, the synthetic strategy involves a photo-induced stereoselective Diels-Alder reaction, which gives only the abnormal <i>trans</i>-fused product as rationalized by density functional theory calculations. Preliminary biological evaluation showed that spirooliganin and regioisomers <b>39</b> exhibited potent inhibition of Coxsackievirus B3. It also revealed the pharmacophore effect of the D-ring (16<i>R</i>,18<i>R</i>,24<i>R</i>, and 26<i>R</i>) for their antiviral activities. Stereochemistry ; Chemistry ; Virus ; Computational biology ; Biology ; Combinatorial chemistry ; Virology Oxidative Organic Chemistry Reactions ; Magnolia and Illicium research ; Traditional and Medicinal Uses of Annonaceae
Authors: Preeyarad Charoensumran | Kornkanya Pratumyot | Tirayut Vilaivan | Thanit Praneenararat
Source: Scientific Reports (article, 2021-06-25)
Field: Chemistry — Spectroscopy

Investigation of key chemical species from durian peduncles and their correlations with durian maturity The popularity and high price of durian make quality control in terms of ripeness very important, which in turn depends heavily on harvesting at an appropriate maturity stage. To date, reports on data-driven methods for maturity prediction are scarce, with many rather focusing on ripeness prediction. Herein, we report the first disclosure of key molecular markers in the liquid extract of durian peduncle that can be a predictive tool for maturity. Multiple chromatographic and spectroscopic techniques including TLC, HPLC, PS-MS, LC-MS/MS, and NMR, were used to characterize chemical profiles of the aqueous extracts from peduncles at different ages. Four compounds that show positive correlations with maturity were identified as sucrose, asparagine, arginine, and pipecolic acid, with asparagine as the most abundant species. This finding paves the way for more research of high impact such as the relationship between biochemical reactions in peduncle and pulp, and the development of accurate and non-destructive sensors for maturity prediction. Ripeness ; Peduncle (anatomy) ; Maturity (psychological) ; Pipecolic acid ; Biology ; Food science ; Botany ; Biochemistry ; Amino acid ; Ripening Analytical Chemistry and Chromatography ; Cultural Heritage Materials Analysis ; Mass Spectrometry Techniques and Applications
Authors: Xiangchun Xu | Xinming Huo | Xiang Qian | Xinqiong Lu | Quan Yu | Kai Ni | Xiaohao Wang
Source: Analytica Chimica Acta (article, 2021-03-13)
Field: Chemistry — Analytical Chemistry

Data-driven and coarse-to-fine baseline correction for signals of analytical instruments Baseline (sea) ; Interpolation (computer graphics) ; SIGNAL (programming language) ; Range (aeronautics) ; Spectrometer ; Algorithm ; Chemistry ; Mixing (physics) ; Computer science ; Artificial intelligence ; Engineering ; Optics Spectroscopy and Chemometric Analyses ; Fault Detection and Control Systems ; Blind Source Separation Techniques