jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Amir H. Tavabi | Paolo Rosi | Raimond B. G. Ravelli | Abril Gijsbers | Enzo Rotunno | Tugrul Guner | Yue Zhang | Alberto Roncaglia | Luca Belsito | Giulio Pozzi | Thibaud Denneulin | Giancarlo Gazzadi | M. R. Ghosh | Stefano Frabboni | Peter J. Peters | Ebrahim Karimi | Peter Tiemeijer | Rafal E. Dunin–Borkowski | Vincenzo Grillo
Source: Zenodo (CERN European Organization for Nuclear Research) (article, 2021-09-30)
Field: Materials Science — Materials Chemistry

Symmetry and planar chirality of a protein measured on an angular basis in a transmission electron microscope In quantum mechanics, each conserved quantity (e.g., energy, position, linear momentum and angular momentum) is associated with a Hermitian operator. Its expected value can then be determined by performing a measurement on the wavefunction. In modern electron microscopy, one can select the initial and final states of the electron and the measurement basis by performing measurements of scattering processes. For example, the orbital angular momentum (OAM) of an electron can be used to reveal the n-fold symmetry of a wavefunction scattered by a sample. Here, we introduce a new composite planar chirality operator that can be used to measure a spiral-like feature in a sample. This concept develops the concept of chirality to highlight a specific roto-scale symmetry. We show that planar chirality can be characterized using an electron OAM sorter to uncover the atomic structures of biomolecules in cryo electron microscopy, either in a stand-alone analysis for fast identification of protein structures or in the context of conventional cryo electron microscopy to produce faster and more detailed 3D reconstructions by solving upside-down orientation ambiguities. Planar ; Basis (linear algebra) ; Chirality (physics) ; Symmetry (geometry) ; Electron microscope ; Transmission electron microscopy ; Planar chirality ; Conventional transmission electron microscope ; Scanning transmission electron microscopy ; Electron ; Transmission (telecommunications) ; Physics ; Optics ; Materials science ; Condensed matter physics ; Chemistry ; Mathematics ; Quantum mechanics ; Computer science ; Geometry ; Symmetry breaking ; Spontaneous symmetry breaking ; Telecommunications ; Computer graphics (images) Enzyme Structure and Function ; Advanced Electron Microscopy Techniques and Applications ; Photosynthetic Processes and Mechanisms
Authors: Ignacy Rzagalinski | Aliona Bogdanova | Bharath Kumar Raghuraman | Eric R. Geertsma | Lena Hersemann | Tjalf Ziemssen | Andrej Shevchenko
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-12-29)
Field: Chemistry — Spectroscopy

FastCAT accelerates absolute quantification of proteins by using multiple short non-purified chimeric standards ABSTRACT Absolute (molar) quantification of clinically relevant proteins determines their reference values in liquid and solid biopsies. FastCAT (for Fast -track Qcon CAT ) method employs multiple short (&lt;50 kDa) stable-isotope labeled chimeric proteins (CPs) composed of concatenated quantotypic (Q-) peptides representing the quantified proteins. Each CP also comprises scrambled sequences of reference (R-) peptides that relate its abundance to a single protein standard (BSA). FastCAT not only alleviates the need in purifying CP or using SDS-PAGE, but also improves the accuracy, precision and dynamic range of the absolute quantification by grouping Q-peptides according to the expected abundance of target proteins. We benchmarked FastCAT against the reference method of MS Western and tested it in the direct molar quantification of neurological markers in the human cerebrospinal fluid at the low ng/mL level. Chemistry ; Chromatography ; Isotope ; Label-free quantification ; Quantitative proteomics ; Proteomics ; Biochemistry ; Physics ; Gene Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Mass Spectrometry Techniques and Applications
Authors: K. V. Andryukov
Source: International Journal of Applied and Fundamental Research (Международный журнал прикладных и фундаментальных исследований) (article, 2021-01-01)
Field: Materials Science — Polymers and Plastics

QUANTITATIVE MODELING OF THE «STRUCTURE-ACTIVITY» OF ANTIMICROBIAL ACTIVITY IN RELATION TO E. COLI USING LIPOPHILICITY AND IONIZATION CONSTANTS OF N-SUBSTITUTED ANTHRANILIC ACIDS КОЛИЧЕСТВЕННОЕ МОДЕЛИРОВАНИЕ «СТРУКТУРА - АКТИВНОСТЬ» ПРОТИВОМИКРОБНОЙ АКТИВНОСТИ ПО ОТНОШЕНИЮ К E. COLI С ИСПОЛЬЗОВАНИЕМ КОНСТАНТ ЛИПОФИЛЬНОСТИИ ИОНИЗАЦИИ Lipophilicity ; Anthranilic acid ; Antimicrobial ; Chemistry ; Ionization ; Computational chemistry ; Stereochemistry ; Organic chemistry ; Ion Polymer Synthesis and Characterization
Authors: Merve Öner | F.T. Tran | Gitte Holm Jensen | Tim Ståhlberg | Kirsten Bisgaard-Frantzen | Stuart M. Stocks | Jens Abildskov | Gürkan Sin
Source: Processes (article, 2021-04-06)
Field: Materials Science — Materials Chemistry

Independent Validation of an In Silico Tool for a Pilot-Scale Pharmaceutical Crystallization Process Development There are many published models for predicting crystal size distribution (CSD) in the literature. However, none of them have been independently and comprehensively tested, which is important for industrial acceptance and confidence of these models. Therefore, in this study, using solubility and kinetic data from the literature, an in silico tool for predicting the crystallization process performance of a model compound system (paracetamol in ethanol) was developed and challenged by independent experiments at the 50 L pilot scale. The solute concentration was tracked, and the final CSD was quantified using three measurement techniques including a novel image analysis tool. The reported parameter uncertainties were also addressed using Monte Carlo simulations. The results showed that, when the models were used within their validity range (e.g., suspended solids), they were able to describe the observed process trends/dynamics (CSD and solute concentration) under varying experimental conditions (cooling time and seed mass) with R2 ranging from 0.72 and 0.90. Overall, the results indicate that, using Monte Carlo simulations to account for known parametric uncertainties, the models can support model-based approaches for crystallization process development from scale-down to scale-up studies as well as control evaluation. Crystallization ; Monte Carlo method ; Parametric statistics ; Scale (ratio) ; Process (computing) ; Process engineering ; Biological system ; In silico ; Computer science ; Environmental science ; Mathematics ; Chemistry ; Thermodynamics ; Engineering ; Statistics ; Physics Crystallization and Solubility Studies ; Process Optimization and Integration ; Chemical and Physical Properties in Aqueous Solutions
Authors: Shimon Ben- Shabat
Source: Significances of Bioengineering & Biosciences (article, 2021-08-31)
Field: Chemistry — Spectroscopy

Influence of Conditions of GC- Flame Ionization Detector Analysis on Parameters of Peaks in Highly Concentrated Compounds The aim of this research was to investigate an influence of flow velocity on the main parameters (retention time, tailing factor, relative area and number of theoretical plates) of peaks belonging to volatile compounds in the GC-Flame ionization detector analysis. Our results showed that as the flow increases, the retention time declines significantly (p<0.01). The other above-mentioned parameters of peaks also change depending on the characteristics of the solvents. The obtained results provide a platform for increasing accuracy of impurity tests for many volatile compounds and development of novel methods of analysis. Flame ionization detector ; Ionization ; Center (category theory) ; Detector ; Analytical Chemistry (journal) ; Library science ; Physics ; Chemistry ; Environmental chemistry ; Gas chromatography ; Chromatography ; Ion ; Optics ; Computer science ; Organic chemistry ; Crystallography Mass Spectrometry Techniques and Applications ; Nuclear Physics and Applications ; Radioactive Decay and Measurement Techniques
Authors: Aaron Oliver | Sheila Podell | Agnieszka Pinowska | Jesse Traller | Sarah R. Smith | Ryan McClure | Alexander S. Beliaev | Pavlo Bohutskyi | Eric A. Hill | Ariel Rabines | Hong Zheng | Lisa Zeigler Allen | Alan Kuo | Igor V. Grigoriev | Andrew E. Allen | David Hazlebeck | Eric E. Allen
Source: Research Square (preprint, 2021-04-08)
Field: Materials Science — Biomaterials

Diploid Genomic Architecture of Nitzschia Hildebrandi, An Elite Biomass Production Diatom Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia hildebrandi . The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum , but 30% smaller than closer relative Fragilariopsis cylindrus . Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. hildebrandi genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production. Phaeodactylum tricornutum ; Biology ; Ploidy ; Diatom ; Nitzschia ; Genome ; Thalassiosira pseudonana ; Genetics ; Genome size ; Botany ; Evolutionary biology ; Gene ; Phytoplankton ; Ecology Diatoms and Algae Research ; Algal biology and biofuel production ; Microbial Community Ecology and Physiology
Authors: Fernando Jiménez‐Grávalos | Dimas Suárez
Source:  (preprint, 2021-06-23)
Field: Chemistry — Physical and Theoretical Chemistry

A Quantum Chemical Topology Picture of Intermolecular Electrostatic Interactions and Charge Penetration Energy Basing on the interacting quantum atoms approach, we present a conceptual and theoretical framework of short-range electrostatic interactions, whose accurate description is still a challenging problem in molecular modeling. For all the non-covalent complexes in the S66 database, the fragment and atomic decomposition of the electrostatic binding energies is performed using both the charge density of the dimers and the unrelaxed densities of the monomers. This energy decomposition together with dispersion corrections gives rise to a pairwise approximation to the total binding energy. It also provides energetic descriptors at varying distance that directly address the atomic and molecular electrostatic interactions as described by point-charge or multipole-based potentials. Additionally, we propose a consistent definition of the charge penetration energy within quantum chemical topology, which is mainly characterized in terms of the intramolecular electrostatic energy. Finally, we discuss some practical implications of our results for the design and validation of electrostatic potentials. Electrostatics ; Multipole expansion ; Electric potential energy ; Intermolecular force ; Intramolecular force ; Chemical physics ; Interaction energy ; Quantum ; Binding energy ; Atoms in molecules ; Quantum chemistry ; Physics ; Topology (electrical circuits) ; Chemistry ; Computational chemistry ; Atomic physics ; Quantum mechanics ; Molecule ; Energy (signal processing) Various Chemistry Research Topics
Authors: Jude Fernandez | B. Bindhu | M. Prabu | K. L. Sandhya
Source: Research Square (preprint, 2021-02-26)
Field: Materials Science — Materials Chemistry

Structural, Morphological and Thermal Decomposition Studies of Calcium and Hafnium Modified BaTiO3 Electro Ceramics Abstract Calcium and hafnium co-doped barium titanate could be used as a replacement for lead zirconate titanate, which is a lead-based ferroelectric material. Solid state reaction accompanied by the usual sintering technique is the classical ceramic-processing method, which demands a lot of time and effort. The present work aims to make the process a lot easier and quicker by employing a modified sol-gel combustion technique to synthesize polycrystalline Ba 0.85 Ca 0.15 Ti (1-x) Hf x O 3 (x=0.00, 0.05, 0.10, 0.15) electro ceramics . The molar ration is fixed at 1:1 for metal and citric acid at pH ~ 1. It was found that Ba 0.85 Ca 0.15 Ti (1-x) Hf x O 3 (where x=0.00, 0.05, 0.10, 0.15) crystallizes completely at around 1000 °C which is much lower than traditional methods. The structure supposedly displays a tetragonal symmetry with the P4mm space group as confirmed through x-ray diffraction (XRD) and Raman spectroscopy. Hafnium ; Materials science ; Ceramic ; Thermal decomposition ; Calcium ; Decomposition ; Metallurgy ; Chemistry ; Zirconium ; Organic chemistry Ferroelectric and Piezoelectric Materials ; Advanced Memory and Neural Computing ; Electronic and Structural Properties of Oxides
Authors: Matej Medvecký | Manolis Mandalakis
Source: Frontiers in Chemistry (article, 2021-08-16)
Field: Chemistry — Spectroscopy

PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires <i>a priori</i> knowledge regarding the optimal peptides to be screened for each protein of interest. In complex, multi-species systems, a specific biochemical process may be driven by a large number of homologous proteins having considerable differences in their amino acid sequence, complicating LC-MS/MS detection. To overcome the complexity of such systems, we have developed an automated pipeline that interrogates UniProt database or user-created protein datasets (e.g. from metagenomic studies) to gather homolog proteins with a defined functional role and extract respective peptide sequences, while it computes several protein/peptide properties and relevant statistics to deduce a small list of the most representative, process-specific and LC-MS/MS-amenable peptides for the microbial enzymatic activity of interest. UniProt ; Computational biology ; Metagenomics ; Proteomics ; Function (biology) ; Protein function ; Biology ; Pipeline (software) ; Peptide ; Computer science ; Bioinformatics ; Gene ; Biochemistry ; Genetics Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Machine Learning in Bioinformatics
Authors: Konstantin Bob | David Teschner | Thomas Kemmer | David Gómez-Zepeda | Stefan Tenzer | Bertil Schmidt | Andreas Hildebrandt
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-07-02)
Field: Chemistry — Spectroscopy

Locality-sensitive hashing enables signal classification in high-throughput mass spectrometry raw data at scale Mass spectrometry is an important experimental technique in the field of proteomics. However, analysis of certain mass spectrometry data faces a combination of two challenges: First, even a single experiment produces a large amount of multi-dimensional raw data and, second, signals of interest are not single peaks but patterns of peaks that span along the different dimensions. The rapidly growing amount of mass spectrometry data increases the demand for scalable solutions. Existing approaches for signal detection are usually not well suited for processing large amounts of data in parallel or rely on strong assumptions concerning the signals properties. In this study, it is shown that locality-sensitive hashing enables signal classification in mass spectrometry raw data at scale. Through appropriate choice of algorithm parameters it is possible to balance false-positive and false-negative rates. On synthetic data, a superior performance compared to an intensity thresholding approach was achieved. The implementation scaled out up to 88 threads on real data. Locality-sensitive hashing is a desirable approach for signal classification in mass spectrometry raw data. Generated data and code are available at https://github.com/hildebrandtlab/mzBucket . Raw data is available at https://zenodo.org/record/5036526 . Computer science ; Raw data ; Locality-sensitive hashing ; Hash function ; Scalability ; Thresholding ; Mass spectrometry ; SIGNAL (programming language) ; Hash table ; Artificial intelligence ; Chemistry ; Database ; Chromatography ; Image (mathematics) Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Mass Spectrometry Techniques and Applications
Authors: S Suganthi. | Dr.k. Pachiyappan
Source: IARJSET (article, 2021-09-22)
Field: Materials Science — Polymers and Plastics

A STUDY ON THE ULTRAVIOLET FINISH ON MODAL /COTTON KNITTED FABRIC USING BIOPOLYMER The well-being of human skin in opposition to ultraviolet radiation is extremely important problem and over current years researches have exposed an increasing curiosity in this field . The growing customer consciousness of the probability of the sun has partial textile industry. This research investigation, the treated and untreated specimen are distingush using FESEM and FT-IR. The value of the treatment is evaluate using the regular tests, such as the ultraviolet protection and UV visible spectrophotometer elements both before and after washing of the treated specimen was also examine. It is get that biopolymer ultraviolet finish able to accurately given to modal/cotton Knitted fabrics. Biopolymer finished specimen showed similar UPF value, providing excellent ultraviolet protection when compared to the untreated specimen. The ultraviolet tests specify a significant improvement in the UV absorbing action in the biopolymer treated fabrics. Biopolymer ; Modal ; Materials science ; Ultraviolet ; Composite material ; Polymer science ; Polymer ; Optoelectronics Polymer Science and PVC
Authors: Teodora DRĂGAN | Luca Liviu Rus | Andrei Cătălin Muntean | A.L. VONICA-TINCU | Ioan Tomuță
Source: Romanian Journal of Pharmaceutical Practice (article, 2021-06-30)
Field: Chemistry — Analytical Chemistry

Quantitative characterisation of extended-release tablets with quetiapine using NIR-chemometric methods This study aims to develop and validate NIR-chemometric methods for quantifying the API (quetiapine) and two excipients in extended-release tablets without sample preparation. The calibration samples were prepared following an experimental design with three variables (quetiapine, HPMC and microcrystalline cellulose) and five levels (concentration 80-90-100-110-120% of API). The validation set included three concentration levels (90-100-110%). The best calibration algorithms have used the same pre-treatment method (SNV), and different factors: 7 PLS factors (R² -0,966 and RMSEP-6,84) for quetiapine, 8 PLS factors (R²-0,927 and RMSEP 6,84) for HPMC and 3 PLS factors (R²-0,983 and RMSEP-7,26) for microcrystalline cellulose. The methods were fully validated according to the ICH guidance using these calibration models. Regarding the trueness of the methods, the recovery was between 98.51 and 99.43 for quetiapine, between 98.61 and 100.85 for HPMC, and between 100.61 and 101.78 for microcrystalline cellulose. According to data obtained, the accuracy profile was ± 5 for quetiapine and HPMC, and ± 6 for microcrystalline cellulose. Linearity profile was also in establish intervals at accuracy and the R2 value was 0.983 for quetiapine, 0.948 for HPMC and 0.997 for microcrystalline cellulose. In conclusion, the developed NIR-chemometric methods have suitable reproducibility, accuracy, linearity and can be used for quantitative characterisation of extended-release tablets with quetiapine, with any sample preparation. Microcrystalline cellulose ; Quetiapine ; Microcrystalline ; Quetiapine Fumarate ; Chromatography ; Cellulose ; Reproducibility ; Calibration ; Materials science ; Chemistry ; Mathematics ; Medicine ; Statistics ; Organic chemistry Spectroscopy and Chemometric Analyses ; Analytical Methods in Pharmaceuticals ; Drug Solubulity and Delivery Systems
Authors: Sopanant Datta | Taweetham Limpanuparb
Source: ChemRxiv (preprint, 2021-05-12)
Field: Chemistry — Organic Chemistry

Steric effects vs electron delocalization: a new look into stability of diastereomers, conformers and constitutional Isomers A quantum chemical investigation of the stability of compounds with identical formulas was carried out on 23 classes of compounds made of C, N, P, O, S atoms as core structures and halogens H, F, Cl, Br, I as substituents. All possible structures were generated and investigated by quantum mechanical methods. The prevalence of formula in which its Z configuration, gauche conformation and meta isomer are the most stable forms is calculated and discussed. Quantitative and qualitative models to explain the stability of the 23 classes of halogenated compounds were also proposed. Diastereomer ; Steric effects ; Electron delocalization ; Conformational isomerism ; Chemistry ; Quantum chemical ; Delocalized electron ; Halogen ; Computational chemistry ; Quantum ; Chemical stability ; Stability (learning theory) ; Crystallography ; Stereochemistry ; Molecule ; Organic chemistry ; Physics ; Quantum mechanics Free Radicals and Antioxidants ; Organic Chemistry Cycloaddition Reactions ; Chemical Reaction Mechanisms
Authors: Julia Contreras‐García
Source: Acta Crystallographica Section A Foundations and Advances (article, 2021-08-14)
Field: Chemistry — Physical and Theoretical Chemistry

Electron density and its interplay with the energy and properties of molecules and solids Electron density has been a great source of insight in the understanding of bonding and structure. Nonetheless, it lacks a fundamental characteristic: its connection to molecular and solid properties is barely predictive. This is so due to the lack of a direct (known) link between electron density and energetics. Molecule ; Electron ; Chemical physics ; Materials science ; Electron density ; Energy (signal processing) ; Physics ; Atomic physics ; Nuclear physics ; Quantum mechanics Various Chemistry Research Topics ; Electron and X-Ray Spectroscopy Techniques ; Advanced Physical and Chemical Molecular Interactions