jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Albert T. Chen | Alexander Franks | Nikolai Slavov
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2018-08-23)
Field: Chemistry — Spectroscopy

DART-ID increases single-cell proteome coverage Abstract Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30 – 50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://github.com/SlavovLab/DART-ID . Author Summary Identifying and quantifying proteins in single cells gives researchers the ability to tackle complex biological problems that involve single cell heterogeneity, such as the treatment of solid tumors. Mass spectrometry analysis of peptides can identify their sequence from their masses and the masses of their fragment ion, but often times these pieces of evidence are insufficient for a confident peptide identification. This problem is exacerbated when analyzing lowly abundant samples such as single cells. To identify even peptides with weak mass spectra, DART-ID incorporates their retention time – the time when they elute from the liquid chromatography used to physically separate them. We present both a novel method of aligning the retention times of peptides across experiments, as well as a rigorous framework for using the estimated retention times to enhance peptide sequence identification. Incorporating the retention time as additional evidence leads to a substantial increase in the number of samples in which proteins are confidently identified and quantified. Dart ; DART ion source ; Proteome ; Tandem mass spectrometry ; Isobaric labeling ; Computational biology ; Mass spectrometry ; Computer science ; Identification (biology) ; Tandem mass tag ; Proteomics ; Chemistry ; Biology ; Chromatography ; Quantitative proteomics ; Bioinformatics ; Biochemistry ; Protein mass spectrometry Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Plamen Daskalov | Eleonora Kirilova | Tsvetelina Georgieva
Source: MATEC Web of Conferences (article, 2018-01-01)
Field: Chemistry — Analytical Chemistry

Performance of an automatic inspection system for classification of Fusarium Moniliforme damaged corn seeds by image analysis This paper presents algorithms for pre-processing, feature selection and classifier design which are used for Parameter Refining in the task of development of an automatic system for recognition and grading of corn seeds with external signs of Fusarium Moniliforme disease. The abilities of several feature selection methods – FDR, Scatter matrices and Stepwise Discriminant Analysis and two classification methods - Support Vector Machine (SVM) and K-Nearest Neighbours (K-NN) are investigated. Design and implementation of the system also has been showed. The system could continually present one by one positioned corn kernels to CCD camera, perform a classification procedure of captured images and discharge seeds to assigned containers. The software was developed in LabVIEW environment including image analysis and classification procedures performed using MATLAB Script. Results for total error rate of 8.4% - 7.2% from preliminary classification related to 8480 seeds from16 Bulgarian varieties and total error rate of 6.95% - 20.4% for experimental results obtained with the system during the control measurements of the seed sample are obtained. Artificial intelligence ; Pattern recognition (psychology) ; Feature selection ; Support vector machine ; Linear discriminant analysis ; Word error rate ; Computer science ; Classifier (UML) ; Software ; MATLAB ; Image processing ; Image (mathematics) Spectroscopy and Chemometric Analyses ; Mycotoxins in Agriculture and Food ; Smart Agriculture and AI
Authors: Sunil Khatak | Mamta Khatak | Faraat Ali | Ashu Rathi | Ravi P. Singh | G. N. Singh | Harish Dureja
Source: Indian Journal of Pharmaceutical Sciences (article, 2018-01-01)
Field: Chemistry — Spectroscopy

Development and Validation of a RP-HPLC Method for Simultaneous Estimation of Antitubercular Drugs in Solid Lipid Nanoparticles A new simple, rapid and sensitive reversed-phase high-performance liquid chromatography method was developed and validated as per International Conference on Harmonization guidelines, Q2 R1, for simultaneous estimation of isoniazid, pyrazinamide and rifampicin in solid lipid nanoparticles. Separation was achieved on a 250×4.6 mm, 5 μm, C-18 column using a linear gradient flow rate of 1.5 ml/min. Isoniazid, pyrazinamide and rifampicin were identified based on their retention times as compared to standards and confirmed with characteristic spectra on a spectrophotometer at 238 nm and eluted at 3.787, 4.173 and 11.273 min, respectively, achieved within 20 min. This method was linear, precise with % RSD values of 0.18 % for isoniazid, 0.15 % for pyrazinamide and 0.47 % for rifampicin, accurate with mean recovery yields of 101.312 % for isoniazid, 99.910 % for pyrazinamide and 99.767 % for rifampicin and selective over the concentration range of 10-150 % for all the three drugs. This method is suitable due to its simplicity and accuracy for routine quality control and stability analysis of antitubercular drugs-loaded solid lipid nanoparticles. Pyrazinamide ; Isoniazid ; Rifampicin ; Chromatography ; Solid lipid nanoparticle ; High-performance liquid chromatography ; Chemistry ; Elution ; Tuberculosis ; Medicine ; Particle size ; Antibiotics Analytical Chemistry and Chromatography ; Analytical Methods in Pharmaceuticals ; Antibiotics Pharmacokinetics and Efficacy
Authors: Fabian Hollaus | Markus Diem | Robert Sablatnig
Source:  (article, 2018-08-01)
Field: Chemistry — Analytical Chemistry

MultiSpectral Image Binarization using GMMs MultiSpectral Imaging enhances the study of degraded historical documents. It allows for visualizing washed out or even invisible ink but also improves the automated analysis because of a denser spectral sampling. We present a new methodology for binarization of multispectral document images that groups spectral signatures of different sources by fitting two Gaussian Mixture Models (GMMs) with Expectation Maximization. Both GMMs assign cluster labels to the multispectral samples and the clustering results are combined for the identification of the handwriting regions. The method is evaluated on the ICDAR 2015 MS-TEx dataset. Results on this publicly available benchmarking set are encouraging. Multispectral image ; Mixture model ; Artificial intelligence ; Pattern recognition (psychology) ; Computer science ; Cluster analysis ; Multispectral pattern recognition ; Expectation–maximization algorithm ; Set (abstract data type) ; Spectral clustering ; Computer vision ; Maximum likelihood ; Mathematics ; Statistics Spectroscopy and Chemometric Analyses ; Image Retrieval and Classification Techniques ; Currency Recognition and Detection
Authors: Erika Piccirillo | Thiago Gerônimo Pires Alegria | Karen Fulan Discola | José Renato Rosa Cussiol | Renato M. Domingos | Marcos Antônio de Oliveira | Leandro de Rezende | Luís Eduardo Soares Netto | Antônia Tavares do Amaral
Source: PLoS ONE (article, 2018-05-21)
Field: Chemistry — Inorganic Chemistry

Structural insights on the efficient catalysis of hydroperoxide reduction by Ohr: Crystallographic and molecular dynamics approaches Organic hydroperoxide resistance (Ohr) enzymes are highly efficient Cys-based peroxidases that play central roles in bacterial response to fatty acid hydroperoxides and peroxynitrite, two oxidants that are generated during host-pathogen interactions. In the active site of Ohr proteins, the conserved Arg (Arg19 in Ohr from Xylella fastidiosa) and Glu (Glu51 in Ohr from Xylella fastidiosa) residues, among other factors, are involved in the extremely high reactivity of the peroxidatic Cys (Cp) toward hydroperoxides. In the closed state, the thiolate of Cp is in close proximity to the guanidinium group of Arg19. Ohr enzymes can also assume an open state, where the loop containing the catalytic Arg is far away from Cp and Glu51. Here, we aimed to gain insights into the putative structural switches of the Ohr catalytic cycle. First, we describe the crystal structure of Ohr from Xylella fastidiosa (XfOhr) in the open state that, together with the previously described XfOhr structure in the closed state, may represent two snapshots along the coordinate of the enzyme-catalyzed reaction. These two structures were used for the experimental validation of molecular dynamics (MD) simulations. MD simulations employing distinct protonation states and in silico mutagenesis indicated that the polar interactions of Arg19 with Glu51 and Cp contributed to the stabilization of XfOhr in the closed state. Indeed, Cp oxidation to the disulfide state facilitated the switching of the Arg19 loop from the closed to the open state. In addition to the Arg19 loop, other portions of XfOhr displayed high mobility, such as a loop rich in Gly residues. In summary, we obtained a high correlation between crystallographic data, MD simulations and biochemical/enzymatic assays. The dynamics of the Ohr enzymes are unique among the Cys-based peroxidases, in which the active site Arg undergoes structural switches throughout the catalytic cycle, while Cp remains relatively static. Xylella fastidiosa ; Chemistry ; Catalytic cycle ; Protonation ; Mutagenesis ; Molecular dynamics ; Active site ; Enzyme ; Catalysis ; Stereochemistry ; Biochemistry ; Mutation ; Biology ; Computational chemistry ; Bacteria ; Genetics ; Organic chemistry Metal-Catalyzed Oxygenation Mechanisms ; Enzyme-mediated dye degradation ; Photosynthetic Processes and Mechanisms
Authors: Fernanda Midori de Oliveira | Marcello Ferreira da Costa | Clésia C. Nascentes | César Ricardo Teixeira Tarley
Source: Journal of environmental chemical engineering (article, 2018-12-20)
Field: Chemistry — Analytical Chemistry

Design of high-performance adsorption cross-linked organic functional polymers towards tricyclic antidepressants using computational simulation Adsorption ; Chemistry ; Polymer ; Methacrylic acid ; Polymer chemistry ; Organic chemistry ; Monomer Analytical chemistry methods development ; Ionic liquids properties and applications ; biodegradable polymer synthesis and properties
Authors: Mahmoud S. Abdelbaset | Mohamed Abdel‐Aziz | Gamal El‐Din A. Abuo‐Rahma | Mohammed Ramadan | Mostafa Abdelrahman
Source: Journal of advanced Biomedical and Pharmaceutical Sciences (article, 2018-12-30)
Field: Chemistry — Organic Chemistry

Pyridazinones and pyrrolones as promising Scaffolds in Medicinal Chemistry Pyridazinones and pyrrolones are important building blocks for some important drugs such as the naturally occurring antibacterial pyrrolone, althiomycin; the cardiotonic pyridazinones, pimobendan and levosimendan and the analgesic anti-inflammatory, emorfozan. Therefore, researchers all over the world paid attention to prepare various pyridazinones and pyrroolones derivatives. The variability in the biological response and ease of preparation from the corresponding furanones attracted attention of researchers to explore these two nuclei in the design and synthesis of different analogues with potential biological actvities. This review article focuses on different biological activities, structure activity relationship and mechanism of action of pyridazinones and pyrrolones derivatives. Chemistry ; Levosimendan ; Combinatorial chemistry ; Pharmacology ; Biology ; Medicine ; Internal medicine Synthesis and Reactions of Organic Compounds ; Synthesis and Biological Evaluation ; Synthesis and biological activity
Authors: Gerard J. Kleywegt | Sameer Velankar | Ardan Patwardhan
Source: FEBS Letters (review, 2018-05-11)
Field: Materials Science — Materials Chemistry

Structural biology data archiving – where we are and what lies ahead For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank, Electron Microscopy Data Bank and Biological Magnetic Resonance Data Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilized to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists. Sketch ; Data science ; Computer science ; Protein Data Bank ; Field (mathematics) ; Biological data ; Treasure ; Data curation ; Function (biology) ; Reliability (semiconductor) ; Biology ; Bioinformatics ; Physics ; Protein structure ; Geography ; Mathematics Enzyme Structure and Function ; Protein Structure and Dynamics ; Advanced Electron Microscopy Techniques and Applications
Authors: Filip Miljković | Jürgen Bajorath
Source: Molecules (article, 2018-09-23)
Field: Chemistry — Organic Chemistry

Data-Driven Exploration of Selectivity and Off-Target Activities of Designated Chemical Probes Chemical probes are of central relevance for chemical biology. To unambiguously explore the role of target proteins in triggering or mediating biological functions, small molecules used as probes should ideally be target-specific; at least, they should have sufficiently high selectivity for a primary target. We present a thorough analysis of currently available activity data for designated chemical probes to address several key questions: How well defined are chemical probes? What is their level of selectivity? Is there evidence for additional activities? Are some probes "better" than others? Therefore, highly curated chemical probes were collected and their selectivity was analyzed on the basis of publicly available compound activity data. Different selectivity patterns were observed, which distinguished designated high-quality probes. Selectivity ; Chemical biology ; Chemistry ; Computational biology ; Relevance (law) ; Small molecule ; Combinatorial chemistry ; Nanotechnology ; Biology ; Biochemistry ; Materials science Click Chemistry and Applications ; Computational Drug Discovery Methods ; Chemical Synthesis and Analysis
Authors: Eri Shimono | Katsuya Inoue | Takio Kurita | Yoji Ichiraku
Source: Chemistry Letters (article, 2018-03-05)
Field: Materials Science — Materials Chemistry

Logistic Regression Analysis for the Material Design of Chiral Crystals Crystal design is one of the biggest dreams of scientists. Currently, statistical methods and artificial intelligence (AI) technology are rapidly developing and suitable for material design. Large-scale crystallographic databases like ICSD are also gathered. Here we demonstrate design of chiral crystals by logistic regression analysis. 689 chiral compounds and 1000 achiral AxBy type compounds (A and B are elements) were used with a true or false chirality dataset. When logistic regression model analysis was applied to all data, it became clear that crystals containing Group 14 or 16 element elements in the crystal become chiral crystals with high probability. These results are consistent with the bonding modes of the elements. Elements in groups 7 (Mn group), 8 (Fe group), 10 (Ni group) and 12 (Zn group) also tended to grow chiral crystals, consistent with the composition of a new chiral magnetic material (Mn–Co–Zn alloy) that has been recently reported (see text). This result implies that logistic regression analysis is useful for the design of chiral crystals. Crystal design is one of scientists’ greatest dreams. Here we demonstrate crystal design using logistic regression analysis. The analysis revealed that group 7 (manganese group), 8 (iron group) and 12 (zinc group), 14 and 16 elements form chiral crystals with high probability. These results are consistent with the bonding modes of the elements. Logistic regression ; Chirality (physics) ; Group (periodic table) ; Chemistry ; Crystal (programming language) ; Crystal structure ; Crystallography ; Manganese ; Mathematics ; Statistics ; Physics ; Organic chemistry ; Computer science ; Chiral symmetry Quasicrystal Structures and Properties ; Magnetic properties of thin films ; Microstructure and mechanical properties
Authors: William P. Schonberg
Source: Aerospace (article, 2018-02-18)
Field: Materials Science — Materials Chemistry

Rupture of a Cryogenic Composite Overwrapped Pressure Vessel Following a High-Speed Particle Impact A primary spacecraft design consideration is the anticipation and mitigation of the possible damage that might occur in the event of an on-orbit micro-meteoroid or orbital debris (MMOD) particle impact. While considerable effort has been expended in the study of non-pressurized spacecraft components under room temperature conditions to MMOD impacts, technical and safety challenges have limited the number of tests that have been conducted on pressurized elements of such spacecraft, especially under cryogenic conditions. This paper presents the development of a data-driven equation for composite material pressure vessels under cryogenic operating conditions that differentiate between impact conditions that, given a tank wall perforation, would result in only a small hole or crack from those that would cause catastrophic tank failure. This equation would be useful to a spacecraft designer who might be able to tailor the design parameters and operating conditions of, for example, a fuel tank so that if such a tank were to be struck and perforated by the impact of an MMOD particle, then only a hole would occur and neither catastrophic spacecraft failure nor additional sizable debris would be created as a result of that impact. Spacecraft ; Perforation ; Aerospace engineering ; Space debris ; Particle (ecology) ; Orbit (dynamics) ; Cabin pressurization ; Engineering ; Environmental science ; Nuclear engineering ; Structural engineering ; Materials science ; Mechanical engineering ; Geology High-Velocity Impact and Material Behavior ; Space Satellite Systems and Control ; Planetary Science and Exploration
Authors: Pierluigi Quagliotto | Andréa Fin
Source: Letters in Organic Chemistry (article, 2018-03-22)
Field: Materials Science — Polymers and Plastics

Advances in Synthetic Methods for the Preparation of Poly(3- hexylthiophene) (P3HT) Synthetic methods for the poly(3-hexylthiophene) polymers (P3HT) preparation were reviewed. Different protocols were reported such as electropolymerization, oxidative method (mainly by FeCl3), Ni-catalyzed methods (McCullough, Rieke, GRIM), Pd- catalyzed methods such as Suzuki and Stille coupling and, the more recent, Direct Arylation Polymerization (DArP). The present review focuses on the synthetic protocols and their relationship to the final key-structural polymer characteristics like regioregularity and molecular weight control which are of importance in the final properties and application of P3HT. An extended literature review was performed covering also very recent advancements. The use of NHC palladium or nickel catalysts, disclosed the door to the preparation of “quasi” living polymers for most of the Ni and Pd catalyzed reactions, enabling a fine tuning of both regioregularity and molecular weight. Keywords: P3HT, conductive polymers, organic synthesis, organic materials, nickel catalyzed reactions, palladium catalyzed reactions. Stille reaction ; Catalysis ; Polymer ; Palladium ; Conductive polymer ; Chemistry ; Nickel ; Polymerization ; Combinatorial chemistry ; Nanotechnology ; Coupling reaction ; Organic synthesis ; Suzuki reaction ; Oxidative coupling of methane ; Polymer chemistry ; Organic chemistry ; Materials science Conducting polymers and applications
Authors: Samraj Mollick | Soumya Mukherjee | Dongwook Kim | Zhiwei Qiao | Aamod V. Desai | Rajat Saha | Yogeshwar D. More | Jianwen Jiang | Myoung Soo Lah | Sujit K. Ghosh
Source: Angewandte Chemie (article, 2018-12-04)
Field: Chemistry — Inorganic Chemistry

Hydrophobic Shielding of Outer Surface: Enhancing the Chemical Stability of Metal–Organic Polyhedra Abstract Metal–organic polyhedra (MOP) are a promising class of crystalline porous materials with multifarious potential applications. Although MOPs and metal–organic frameworks (MOFs) have similar potential in terms of their intrinsic porosities and physicochemical properties, the exploitation of carboxylate MOPs is still rudimentary because of the lack of systematic development addressing their chemical stability. Herein we describe the fabrication of chemically robust carboxylate MOPs via outer‐surface functionalization as an a priori methodology, to stabilize those MOPs system where metal–ligand bond is not so strong. Fine‐tuning of hydrophobic shielding is key to attaining chemical inertness with retention of the framework integrity over a wide range of pH values, in strong acidic conditions, and in oxidizing and reducing media. These results are further corroborated by molecular modelling studies. Owing to the unprecedented transition from instability to a chemically ultra‐stable regime using a rapid ambient‐temperature gram‐scale synthesis (within seconds), a prototype strategy towards chemically stable MOPs is reported. Oxidizing agent ; Surface modification ; Chemical stability ; Chemistry ; Carboxylate ; Metal-organic framework ; Chemical engineering ; Metal ; Ligand (biochemistry) ; Porosity ; Transition metal ; Electromagnetic shielding ; Nanotechnology ; Combinatorial chemistry ; Materials science ; Adsorption ; Organic chemistry ; Physical chemistry ; Catalysis ; Composite material Metal-Organic Frameworks: Synthesis and Applications ; Nanoplatforms for cancer theranostics ; Covalent Organic Framework Applications