jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Sidra Hussan Saeed | Ghulam Mujtaba Shah | Uneb Gazder | Shahida Shaheen | Khalid F. Almutairi | Graciela Dolores Ávila-Quezada | Abeer Hashem | Elsayed Fathi Abd Allah | Qaisar Mahmood
Source: Preprints.org (preprint, 2023-06-29)
Field: Chemistry — Analytical Chemistry

Individual and Combined Influences of Copper, Cadmium and Arsenic on the Total Phenolic and Flavonoid Contents in Various Tissues of &lt;em&gt;Hydrocotyle umbellata &lt;/em&gt;L. Heavy metals toxicity is a grave environmental issue in contemporary times. Phytoremediation is economic, effective and ecofriendly approach to decontaminate and remediate metal contaminated areas. Phenolic and Flavonoid content are important abiotic stress markers. The individual and combined impacts of toxiferous metals Arsenic (As), Cadmium (Cd) and (Copper) Cu were employed in recent studies to investigate their effect on Total flavonoids content (TFC) and total phenolic content (TPC) in various parts of Hydrocotyle umbellata L. to explore the role of plant in abating metal contamination. Folin- ciocalteu and AlCl 3 methods were used for investigating TPC and TFC respectively. Two-way ANOVA and CART model were employed for statistical analysis. Highest TPC was examined in decreasing order as leaf &amp;amp;amp; gt; stem &amp;amp;amp; gt; root in case of all the metals. Whereas highest TFC was found in all plant parts when subjected to As toxicity, and the lowest TFC was found in stem of the plant in respect to Cu toxicity. There was significant effect on TPC on plant part when subjected to Cu and As stress, but so significance was observed in plant part in case of Cd and combined metal stress. Treatment concentration had no significant effect on TPC when subjected to unique impact of all the three metals but had significant effect in case of combined metal stress. Similarly, in case of TFC no significant effect was recorded in case of plant part in all the stress types. But treatment amount has significant impact on Cd and combined metal stress. Metal type has significant effect on TPC and TFC. Whereas plant part has significant impact on TPC but non-significant values were observed on TFC in this case. This study epitomizes TPC and TFC in plants as effective and viable tool to pertain their role in phytoremediation against metal contamination. Therefore H. umbellata L. can be exerted for successful assemblage and decontamination of Cd, Cu and As in different plant parts. Arsenic ; Cadmium ; Phytoremediation ; Chemistry ; Flavonoid ; Metal ; Copper ; Toxicity ; Copper toxicity ; Metal toxicity ; Horticulture ; Environmental chemistry ; Heavy metals ; Botany ; Biology ; Biochemistry ; Organic chemistry Heavy Metals in Plants
Authors: Nikolas R. Burton | Daniel A. Polasky | Flowreen Shikwanna | Samuel Ofori | Tianyang Yan | Daniel Geiszler | Felipe da Veiga Leprevost | Alexey I. Nesvizhskii | Keriann M. Backus
Source: ChemRxiv (preprint, 2023-02-27)
Field: Chemistry — Spectroscopy

A solid-phase compatible silane-based cleavable linker enables custom isobaric quantitative chemoproteomics The human proteome harbors tens of thousands of ligandable or potentially druggable cysteine residues. Consequently, pinpointing the optimal covalent molecule for each cysteine residue is a key challenge for chemical probe and drug discovery campaigns. While chemoproteomic methods have enabled proteome-wide screens of electrophilic molecules, achieving comprehensive proteome-wide structure activity relationship (SAR) maps requires technical innovation in two key areas: (1) streamlined sample preparation workflows and (2) increased sample throughput via multiplexing. Recent inroads in the latter challenge have been made through the incorporation of isobaric tandem mass tags (TMT) into chemoproteomic workflows; the high cost and late-stage isobaric labeling collectively have, however, limited adoption of such MS2/MS3-based quantitation strategies. Here we report the silane-based Cleavable Linkers for Isotopically-labeled Proteomics (sCLIP) method, which harnesses custom isotopically labeled chemoproteomic capture reagents to simplify sample preparation and achieve low cost 6-plex isobaric multiplexing. The sCLIP method is enabled by a high yielding and scalable route to dialkoxydiphenylsilane fluorenylmethyloxycarbonyl (DADPS-Fmoc) protected amino acid building blocks, which enable facile synthesis of customizable, isotopically labeled, and chemically cleavable biotin capture reagents. Benchmarking of a panel of fully functionalized sCLIP capture reagents revealed performance comparable to established platforms. Using the diagnostic ion mining of the FragPipe computational pipeline, we identified a characteristic fragment ion with suitable intensity and specificity for tandem mass spectrometry (MS2)-based quantification. By harnessing this unprecedented gas phase chemistry, we established a cost-effective high performance 6-plex isobaric reagent set in which the mass balancer and reporter are encoded in the cysteine-capping and biotin capture reagents, respectively. Application of the sCLIP reagents to chemoproteomic analysis of electrophilic molecules uncovered 4805 total ligandable cysteines, including established and unprecedented cysteine-ligand pairs. Isobaric process ; Proteome ; Isobaric labeling ; Tandem mass tag ; Computer science ; Chemistry ; Combinatorial chemistry ; Proteomics ; Tandem mass spectrometry ; Quantitative proteomics ; Mass spectrometry ; Computational biology ; Nanotechnology ; Chromatography ; Materials science ; Biochemistry ; Biology ; Protein mass spectrometry ; Physics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Chemical Synthesis and Analysis
Authors: Marco Carratù | V. Gallo | Valerio Laino | Consolatina Liguori
Source:  (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

Use of Artificial Intelligence in optical microscope imaging Identification and morphological analysis of microorganisms are of high interest in scientific research, especially in the medical field and food industry.Identification allows rapid functional characterization based on similarities with known related species enabling to confirm the identity of an isolate used, for example, in a trademarked industrial process.Monitoring of microorganisms within a given ecosystem and analysis of the morphological characteristics of the observed species enable quality control of the process under analysis.Such procedures are carried out manually in specialized laboratories by trained personnel using the appropriate optical equipment; therefore, it may be of great interest to use automatic measurement approaches that enable rapid and effective process analysis.Artificial intelligence techniques in computer vision and especially deep learning are well suited for this purpose.This article describes the realization of an automatic measurement system based on deep learning for the identification and measurement of morphological parameters of Saccharomyces cerevisiae microorganisms present in brewer's yeast by returning for each of the objects identified within the image the confidence score, the coordinates, and the dimensions of the corresponding ellipsoid-shaped cell.The metrological characteristics of the system have been defined through a calibration process by comparing measurements with a reference system. Artificial intelligence ; Identification (biology) ; Computer science ; Process (computing) ; Calibration ; Computer vision ; Machine learning ; Mathematics ; Ecology ; Biology Spectroscopy and Chemometric Analyses ; Identification and Quantification in Food ; Fermentation and Sensory Analysis
Authors: Andreas Erbs Hillers‐Bendtsen | Jacob Lynge Elholm | Oscar Berlin Obel | Helen Hölzel | Kasper Moth‐Poulsen | Kurt V. Mikkelsen
Source: Angewandte Chemie (article, 2023-07-25)
Field: Materials Science — Materials Chemistry

Searching the Chemical Space of Bicyclic Dienes for Molecular Solar Thermal Energy Storage Candidates Abstract Photoswitches are molecular systems that are chemically transformed subsequent to interaction with light and they find potential application in many new technologies. The design and discovery of photoswitch candidates require intricate molecular engineering of a range of properties to optimize a candidate to a specific applications, a task which can be tackled efficiently using quantum chemical screening procedures. In this paper, we perform a large scale screening of approximately half a million bicyclic diene photoswitches in the context of molecular solar thermal energy storage using ab initio quantum chemical methods. We further device an efficient strategy for scoring the systems based on their predicted solar energy conversion efficiency and elucidate potential pitfalls of this approach. Our search through the chemical space of bicyclic dienes reveals systems with unprecedented solar energy conversion efficiencies and storage densities that show promising design guidelines for next generation molecular solar thermal energy storage systems. Photoswitch ; Context (archaeology) ; Chemical space ; Bicyclic molecule ; Energy transformation ; Energy storage ; Chemistry ; Quantum chemical ; Nanotechnology ; Materials science ; Physics ; Molecule ; Organic chemistry ; Thermodynamics ; Drug discovery Photochromic and Fluorescence Chemistry ; Molecular Junctions and Nanostructures ; Organic Electronics and Photovoltaics
Authors: Gang Seob Jung | Yoshihide Yoshimoto | Kwang Jin Oh | Shinji Tsuneyuki
Source: arXiv (Cornell University) (preprint, 2023-08-16)
Field: Materials Science — Materials Chemistry

Extended Ensemble Molecular Dynamics for Thermodynamics of Phases The first-order phase transitions and related thermodynamics properties are primary concerns of materials sciences and engineering. In traditional atomistic simulations, the phase transitions and the estimation of their thermodynamic properties are challenging tasks because the trajectories get trapped in local minima close to the initial states. In this study, we investigate various extended ensemble molecular dynamics (MD) methods based on the multicanonical ensemble method using the Wang-Landau (WL) approach. We performed multibaric-multithermal (MBMT) method to fluid phase, gas-liquid transition, and liquid-solid transition of the Lennard-Jones (LJ) system. The derived thermodynamic properties of the fluid phase and the gas-liquid transition from the MBMT agree well with the previously reported equation of states (EOSs). However, the MBMT cannot correctly predict the liquid-solid transition. The multiorder-multithermal (MOMT) ensemble shows significantly enhanced sampling between liquid and solid states with an accurate estimation of transition temperatures. We further investigated the dynamics of each system based on their free energy shapes, providing fundamental insights for their sampling behaviors. This study guides the prediction of broader crystalline materials, e.g., alloys, for their phases and thermodynamic properties from atomistic modeling. Molecular dynamics ; Phase transition ; Thermodynamics ; Maxima and minima ; Statistical physics ; Thermodynamic integration ; Umbrella sampling ; Materials science ; Chemistry ; Physics ; Computational chemistry ; Mathematics Machine Learning in Materials Science ; Protein Structure and Dynamics ; Phase Equilibria and Thermodynamics
Authors: Fatma Demirkaya Miloğlu | Burak Bayrak | Yücel Kadıoğlu
Source: Chemistry Africa (article, 2023-05-03)
Field: Chemistry — Spectroscopy

Determination of Isoniazid Gained Fluorescent with 9-Anthraldehyde by HPLC-FL Method in Dosage Forms High-performance liquid chromatography ; Isoniazid ; Detection limit ; Chromatography ; Chemistry ; Mycobacterium tuberculosis ; Tuberculosis ; Fluorescence ; Dosage form ; Chromatography detector ; Medicine Analytical Chemistry and Chromatography ; Analytical Methods in Pharmaceuticals ; Antibiotics Pharmacokinetics and Efficacy
Authors: Paolo Inaudi | Ornella Abollino | Monica Argenziano | Mery Malandrino | Caterina Guiot | Stefano Bertinetti | Laura Favilli | Agnese Giacomino
Source: Preprints.org (preprint, 2023-10-04)
Field: Chemistry — Electrochemistry

Advancements in Portable Voltammetry: A Promising Approach for Iron Speciation Analysis Iron, a crucial element in our environment, plays a vital role in numerous natural processes. Understanding the presence and concentration of iron in the environment is very important, as it impacts various aspects of our planet’s health. On-site detection and speciation of iron are significant for several reasons. In this context, the present work aims to evaluate the applicability of voltammetry for on-site determination of iron and its possible speciation using a portable voltammetric analyzer. Voltammetry offers the advantage of convenience and cost-effectiveness. For iron (III) determination a modification of a glassy carbon electrode (GCE) with an antimony-bismuth film (SbBiFE) using acetate buffer (pH=4) as supporting electrolyte was used. The technique adopted was Square Wave Adsoptive Cathodic Stripping Voltammetry (SW-AdCSV) and we used 1-(2-piridylazo)-2-naphthol (PAN) as iron (III) ligand. Linearity, repeatability, detection limit and accuracy were determined using synthetic solutions, then a Standard Reference Material (SRM) 1643f - Trace Elements in Water was used for validation measurements in real matrix. The procedure was finally applied to real samples (tap, lake and sea water) and the results obtained were compared by Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES). The results obtained demonstrated the excellent applicability of the proposed on-site voltammetric procedure for the determination of iron and its speciation in water. Cathodic stripping voltammetry ; Voltammetry ; Detection limit ; Tap water ; Anodic stripping voltammetry ; Context (archaeology) ; Analytical Chemistry (journal) ; Supporting electrolyte ; Chemistry ; Repeatability ; Seawater ; Materials science ; Environmental chemistry ; Electrolyte ; Electrode ; Electrochemistry ; Environmental science ; Chromatography ; Environmental engineering Electrochemical Analysis and Applications ; Water Quality Monitoring and Analysis
Authors: Marco A. Arriaga | Juan A. Amieva | Jaqueline Quintanilla | Angela Jimenez | Julio Ledezma | Silverio A Lopez | Karen S. Martirosyan | Sue Anne Chew
Source: Biotechnology and Bioengineering (article, 2023-08-22)
Field: Materials Science — Biomaterials

The application of electrosprayed minocycline‐loaded PLGA microparticles for the treatment of glioblastoma The survival of patients with glioblastoma multiforme (GBM), the most common and invasive form of malignant brain tumors, remains poor despite advances in current treatment methods including surgery, radiotherapy, and chemotherapy. Minocycline is a semi-synthetic tetracycline derivative that has been widely used as an antibiotic and more recently, it has been utilized as an antiangiogenic factor to inhibit tumorigenesis. The objective of this study was to investigate the utilization of electrospraying process to fabricate minocycline-loaded poly(lactic-co-glycolic acid) (PLGA) microparticles with high drug loading and loading efficiency and to evaluate their ability to induce cell toxicity in human glioblastoma (i.e., U87-MG) cells. The results from this study demonstrated that solvent mixture of dicholoromethane (DCM) and methanol is the optimal solvent combination for minocycline and larger amount of methanol (i.e., 70:30) resulted in a higher drug loading. All three solvent ratios of DCM:methanol tested produced microparticles that were both spherical and smooth, all in the micron size range. The electrosprayed microparticles were able to elicit a cytotoxic response in U87-MG glioblastoma cells at a lower concentration of drug compared to the free drug. This work provides proof of concept to the hypothesis that electrosprayed minocycline-loaded PLGA microparticles can be a promising agent for the treatment of GBM and could have potential application for cancer therapies. Minocycline ; PLGA ; Glioma ; Glioblastoma ; Glycolic acid ; Toxicity ; Drug ; Pharmacology ; Chemistry ; Cancer research ; Materials science ; Nanoparticle ; Lactic acid ; Antibiotics ; Medicine ; Nanotechnology ; Biochemistry ; Organic chemistry ; Biology Nanoparticle-Based Drug Delivery ; Graphene and Nanomaterials Applications ; Electrohydrodynamics and Fluid Dynamics
Authors: Е. О. Бахрушина | V. S. Pyzhov | P. S. Sakharova | Н. Б. Демина | D. A. Chizhova | T. V. Tabanskaya | M. F. Lutfullin
Source: The Bulletin of the Scientific Centre for Expert Evaluation of Medicinal Products Regulatory Research and Medicine Evaluation (article, 2023-06-29)
Field: Materials Science — Biomaterials

Block Copolymers of Ethylene Oxide and Propylene Oxide: Prospects for Medical and Pharmaceutical Application in Russia Block copolymers of ethylene oxide and propylene oxide (EO/PO block copolymers) are polymeric non-ionic surfactants with a high hydrophilic–lipophilic balance also referred to as pluronics, poloxamers, or proxanols. These compounds are among the most demanded modern excipients for the production of medicines. EO/PO block copolymers are used both in the production of traditional (liquid, semi-solid, and solid) dosage forms and as part of targeted delivery systems. The extensive application of EO/PO block copolymers is due to the diverse array of their properties, including not only solubilising, emulsifying, gelling, and other effects but also thermoreversibility, which is essential for developing in situ delivery systems and 3D printing technologies. The aim of the study was to evaluate the potential of EO/PO block copolymers for medicinal use and to assess the range of medicinal products approved in the Russian Federation that contain EO/PO block copolymers. This review presents an analysis of the register of poloxamer-containing medicines approved in the Russian Federation, a list of the largest manufacturers of EO/PO block copolymers in the world, and a study of the possibility to use copolymers for medical purposes. Currently, there are more than 10 chemical manufacturers producing EO/PO block copolymers for the pharmaceutical, biotechnology, and other industries around the world. EO/PO block copolymers are included in more than 60 medicinal products present in the Russian pharmaceutical market; this observation indicates the need to phase out the import of poloxamers. Copolymer ; Propylene oxide ; Poloxamer ; Ethylene oxide ; Oxide ; Materials science ; Chemistry ; Organic chemistry ; Polymer biodegradable polymer synthesis and properties ; Chemical Synthesis and Reactions ; Advanced Polymer Synthesis and Characterization
Authors: Xuanyu Zhu | Marc Riera | Ethan F. Bull-Vulpe | Francesco Paesani
Source: ChemRxiv (preprint, 2023-03-22)
Field: Materials Science — Materials Chemistry

MB-pol(2023): Sub-chemical accuracy for water simulations from the gas to the liquid phase We use the MB-pol theoretical/computational framework to introduce a new family of data- driven many-body potential energy functions (PEFs) for water, named MB-pol(2023). By employing larger 2-body and 3-body training sets, including an explicit machine-learned representation of 4-body energies, and adopting more sophisticated machine-learned representations of 2-body and 3-body energies, we demonstrate that the MB-pol(2023) PEFs achieve sub-chemical accuracy in modeling the energetics of the hexamer isomers, outperforming both the original MB-pol and q-AQUA PEFs, which currently provide the most accurate description of water clusters in the gas phase. Importantly, the MB-pol(2023) PEFs provide remarkable agreement with the experimental results for various properties of liquid water, improving upon the original MB-pol PEF and effectively closing the gap with experimental measurements. Random hexamer ; Water body ; Gas phase ; Liquid phase ; Liquid water ; Chemistry ; Physics ; Thermodynamics ; Environmental science ; Crystallography ; Environmental engineering Machine Learning in Materials Science ; Protein Structure and Dynamics ; Spectroscopy and Quantum Chemical Studies
Authors: Kaleb J. Duelge | Joshua A. Young
Source: Biomedical Materials & Devices (article, 2023-09-06)
Field: Chemistry — Spectroscopy

Estimating Recovery in the Liquid–Liquid Extraction Chemical Space Robustness (evolution) ; Extraction (chemistry) ; Computer science ; Analyte ; Chromatography ; Biological system ; Process engineering ; Materials science ; Chemistry ; Engineering Analytical Chemistry and Chromatography ; Chemical and Physical Properties in Aqueous Solutions ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Rune D. Kjærsgaard | Aaron Bello-Arufe | Alexander D. Rathcke | Lars A. Buchhave | Line Katrine Harder Clemmensen
Source: Astronomy and Astrophysics (article, 2023-07-31)
Field: Chemistry — Organic Chemistry

TAU: A neural network based telluric correction framework Context. Telluric correction is one of the critically important outstanding issues for extreme precision radial velocities and exoplanet atmosphere observations. Thorough removal of small so-called micro tellurics across the entire wavelength range of optical spectro-graphs is necessary in order to reach the extreme radial velocity precision required to detect Earth-analog exoplanets orbiting in the habitable zone of solar-type stars. Likewise, proper treatment of telluric absorption will be important for exoplanetary atmosphere observations with high-resolution spectrographs on future extremely large telescopes (ELTs). Aims. In this work, we introduce the Telluric AUtoencoder ( TAU ). TAU is an accurate high-speed telluric correction framework built to extract the telluric spectrum with previously unobtained precision in a computationally efficient manner. Methods. TAU is built on a neural network autoencoder trained to extract a highly detailed telluric transmission spectrum from a large set of high-precision observed solar spectra. We accomplished this by reducing the data into a compressed representation, allowing us to unveil the underlying solar spectrum and simultaneously uncover the different modes of variation in the observed spectra relating to the absorption from H 2 O and O 2 in the atmosphere of Earth. Results. We demonstrate the approach on data from the HARPS-N spectrograph and show how the extracted components can be scaled to remove H 2 O and O 2 telluric contamination with improved accuracy and at a significantly lower computational expense than the current state of the art synthetic approach molecfit . We also demonstrate the capabilities of TAU to remove telluric contamination from observations of the ultra-hot Jupiter HAT-P-70b allowing for the retrieval of the atmospheric signal. We publish the extracted components and an open-source code base allowing scholars to apply TAU on their own data. Physics ; Astrophysics ; Artificial neural network ; Astronomy ; Artificial intelligence Chemical Thermodynamics and Molecular Structure ; Geochemistry and Geologic Mapping ; Spectroscopy and Chemometric Analyses