jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Khalid A. Al‐Gaadi | Abdalhaleem A. Hassaballa | Rangaswamy Madugundu | ElKamil Tola | Ronnel Fulleros
Source: Current Science (article, 2020-09-25)
Field: Chemistry — Analytical Chemistry

Prediction of Potato High-Yield Zones of a Field:Bivariate Frequency Ratio Technique Bivariate frequency ratio (BFR) technique was employed to determine high-yield zones in a 30 ha potato (Solanum tuberosum L.) field located in Wadi-Ad-Dawasir, Saudi Arabia. BFR was performed by inputting selected yield tendency factors (YTFs) and potato actual yield (Y A ). The YTFs were NDVIderived from Sentinel-2 images, soil electrical conductivity, nitrogen, pH and texture. The obtained yield tendency map (Y P ) was assessed against Y A using the area under the curve metric. Although low accuracy (41-58%) was observed with the individual YTFs, high-yield zones were determined with an accuracy of 90% using the cumulative response of YTFs. Bivariate analysis ; Yield (engineering) ; Environmental science ; Field (mathematics) ; Statistics ; Agronomy ; Mathematics ; Geology ; Biology ; Materials science ; Metallurgy Spectroscopy and Chemometric Analyses
Authors: Praveen Kumar
Source: Preprints.org (preprint, 2020-11-25)
Field: Materials Science — Materials Chemistry

&lt;strong&gt;Role of Nanoscience in Agriculture&lt;/strong&gt; Nanoparticles are widely used in the agricultural sector because of their distinctive properties. Studies have shown the influence of nanoparticles on plant growth and production. Nanoparticles act as effective carriers in the delivery of agrochemicals to plants. They provide site targeted delivery of nutrients and thus, prevents wastage of nutrients applied for plant growth and productivity. Bioremediation of pollutants is an emerging technology that provides bio-nano materials for the protection of agriculture from pollution. The aim of this review is to present and focus on the latest techniques used for the reduction of environmental pollution and improved agricultural production. This review speculates about the biosynthesis of nanomaterials from different sources like plants, fungi, and bacteria along with chemical and organic synthesis from carbon, silver, and gold. The role of nanoscience in detecting plant diseases and the removal of heavy metals. Application of Nanoscience in storing, production, processing, and transport of agricultural materials. It is also emphasized that Nanoscience may transform agriculture through the innovation of new techniques like Precision farming, improvement of plants to engross nutrients, targeted use of inputs, detection and control of diseases and withstand environmental pressures. Further, efforts have been made in describing that nanoparticles may act as a better substitute for agricultural plant growth and nutrition improvement by lowering the content of pollutants and pre-detection of diseases in plants. The biosynthetic route of nanomaterial synthesis could emerge as a better and safer option for environmental pollution reduction. Thus, nanoscience may increase agricultural production to feed a huge population in near future. Agriculture ; Agrochemical ; Pollutant ; Environmental pollution ; Productivity ; Environmental science ; Agricultural productivity ; Pollution ; Nanotechnology ; Biotechnology ; Environmental protection ; Materials science ; Ecology ; Biology Nanoparticles: synthesis and applications
Authors: Mulatu Yohannes Nanusha | Martin Krauß | Carina D. Schönsee | Barbara F. Günthardt | Thomas D. Bucheli | Werner Brack
Source: Research Square (preprint, 2020-09-09)
Field: Chemistry — Organic Chemistry

Target screening of plant secondary metabolites in river waters by liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS) Abstract Background: Substantial efforts have been made to monitor potentially hazardous anthropogenic contaminants in surface waters while for plant secondary metabolites (PSMs) almost no data on occurrence in the water cycle are available. These metabolites enter river waters through various pathways such as leaching, surface run-off and rain sewers or input of litter from vegetation and might add to the biological activity of the chemical mixture. To reduce this data gap we conducted a LC-HRMS target screening in river waters from two different catchments for 150 plant metabolites which were selected from a larger database considering their expected abundance in the vegetation, their potential mobility, persistence and toxicity in the water cycle and commercial availability of standards. Results : The screening revealed the presence of 12 out of 150 possibly toxic PSMs including coumarins (bergapten, scopoletin, fraxidin, esculetin and psoralen), a flavonoid (formononetin) and alkaloids (lycorine and narciclasine). The compounds narciclasine and lycorine were detected at concentrations up to 3 µg/L while esculetin and fraxidin occurred at concentrations above 1 µg/L. Nine compounds occurred at concentrations above 0.1 µg/L, the Threshold for Toxicological Concern (TTC) for non-genotoxic and non-endocrine disrupting chemicals in drinking water. Conclusions : Our study provides an overview of potentially biologically active PSMs in surface waters and recommends their consideration in monitoring and risk assessment of water resources. This is currently hampered by a lack of effect data including toxicity to aquatic organisms, endocrine disruption and genotoxicity and demands for involvement of these compounds in biotesting. Mass spectrometry ; Chromatography ; Resolution (logic) ; Chemistry ; Liquid chromatography–mass spectrometry ; High resolution ; Environmental chemistry ; Geology ; Remote sensing ; Computer science Chemical synthesis and alkaloids ; Allelopathy and phytotoxic interactions ; Alkaloids: synthesis and pharmacology
Authors: Yuyi Feng | P. Leǐderer | Rongxuan Zhao | Xiaofei Xiao | Vincenzo Giannini | Stefan A. Maier | Clayton A. Nemitz | Zemeng Lin | Ning Ding | Guoguo Kang | Dewen Cheng | Lukas Schmidt‐Mende | Lingling Huang | Yongtian Wang
Source: Optics Express (article, 2020-08-25)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Giant polarization anisotropic optical response from anodic aluminum oxide templates embedded with plasmonic metamaterials Plasmonic metamaterials enable extraordinary manipulation of key constitutive properties of light at a subwavelength scale and thus have attracted significant interest. Here, we report a simple and convenient nanofabrication method for a novel meta-device by glancing deposition of gold into anodic aluminum oxide templates on glass substrates. A methodology with the assistance of ellipsometric measurements to examine the anisotropy and optical activity properties is presented. A tunable polarization conversion in both transmission and reflection is demonstrated. Specifically, giant broadband circular dichroism for reflection at visible wavelengths is experimentally realized by oblique incidence, due to the extrinsic chirality resulting from the mutual orientation of the metamaterials and the incident beam. This work paves the way for practical applications for large-area, low-cost polarization modulators, polarization imaging, displays, and bio-sensing. Metamaterial ; Materials science ; Optics ; Plasmon ; Optoelectronics ; Polarization (electrochemistry) ; Circular polarization ; Nanophotonics ; Nanolithography ; Photonic metamaterial ; Surface plasmon ; Extraordinary optical transmission ; Ray ; Surface plasmon polariton ; Fabrication ; Physics Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Optical Coatings and Gratings
Authors: Benjamín J. Sánchez | Petri‐Jaan Lahtvee | Kate Campbell | Sergo Kasvandik | Rosemary Yu | Iván Domenzain | Aleksej Zelezniak | Jens Nielsen
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-03-24)
Field: Chemistry — Spectroscopy

Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in <i>Saccharomyces cerevisiae</i> Abstract Protein quantification via label-free mass spectrometry (MS) has become an increasingly popular method for determining genome-wide absolute protein abundances. A known caveat of this approach is the poor technical reproducibility, i.e. how consistent the estimations are when the same sample is measured repeatedly. Here, we measured proteomics data for Saccharomyces cerevisiae with both biological and inter-batch technical triplicates, to analyze both accuracy and precision of protein quantification via MS. Moreover, we analyzed how these metrics vary when applying different methods for converting MS intensities to absolute protein abundances. We found that a simple normalization and rescaling approach performs as accurately yet more precisely than methods that rely on external standards. Additionally, we show that inter-batch reproducibility is worse than biological reproducibility for all evaluated methods. These results subsequently serve as a benchmark for assessing MS data quality for protein quantification, whilst also underscoring current limitations in this approach. Reproducibility ; Normalization (sociology) ; Quantitative proteomics ; Benchmarking ; Benchmark (surveying) ; Saccharomyces cerevisiae ; Proteomics ; Computer science ; Accuracy and precision ; Mass spectrometry ; Biological system ; Data mining ; Chemistry ; Statistics ; Chromatography ; Mathematics ; Biology ; Genetics ; Yeast Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Sandeep Kasaragod | Varshasnata Mohanty | Ankur Tyagi | Santosh Kumar Behera | Arun H. Patil | Sneha M. Pinto | Thottethodi Subrahmanya Keshava Prasad | Prashant Kumar Modi | Harsha Gowda
Source: F1000Research (preprint, 2020-05-11)
Field: Chemistry — Spectroscopy

CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets <ns4:p>Cancer genome sequencing studies have revealed a number of variants in coding regions of several genes. Some of these coding variants play an important role in activating specific pathways that drive proliferation. Coding variants present on cancer cell surfaces by the major histocompatibility complex serve as neo-antigens and result in immune activation. The success of immune therapy in patients is attributed to neo-antigen load on cancer cell surfaces. However, which coding variants are expressed at the protein level can’t be predicted based on genomic data. Complementing genomic data with proteomic data can potentially reveal coding variants that are expressed at the protein level. However, identification of variant peptides using mass spectrometry data is still a challenging task due to the lack of an appropriate tool that integrates genomic and proteomic data analysis pipelines. To overcome this problem, and for the ease of the biologists, we have developed a graphical user interface (GUI)-based tool called CusVarDB. We integrated variant calling pipeline to generate sample-specific variant protein database from next-generation sequencing datasets. We validated the tool with triple negative breast cancer cell line datasets and identified 423, 408, 386 and 361 variant peptides from BT474, MDMAB157, MFM223 and HCC38 datasets, respectively.</ns4:p> Computational biology ; Genome ; Major histocompatibility complex ; Biology ; Gene ; Bioinformatics ; Computer science ; Genetics Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; RNA and protein synthesis mechanisms
Authors: Sandeep Kasaragod | Varshasnata Mohanty | Ankur Tyagi | Santosh Kumar Behera | Arun H. Patil | Sneha M. Pinto | Thottethodi Subrahmanya Keshava Prasad | Prashant Kumar Modi | Harsha Gowda
Source: F1000Research (preprint, 2020-11-16)
Field: Chemistry — Spectroscopy

CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets Cancer genome sequencing studies have revealed a number of variants in coding regions of several genes. Some of these coding variants play an important role in activating specific pathways that drive proliferation. Coding variants present on cancer cell surfaces by the major histocompatibility complex serve as neo-antigens and result in immune activation. The success of immune therapy in patients is attributed to neo-antigen load on cancer cell surfaces. However, which coding variants are expressed at the protein level can't be predicted based on genomic data. Complementing genomic data with proteomic data can potentially reveal coding variants that are expressed at the protein level. However, identification of variant peptides using mass spectrometry data is still a challenging task due to the lack of an appropriate tool that integrates genomic and proteomic data analysis pipelines. To overcome this problem, and for the ease of the biologists, we have developed a graphical user interface (GUI)-based tool called CusVarDB. We integrated variant calling pipeline to generate sample-specific variant protein database from next-generation sequencing datasets. We validated the tool with triple negative breast cancer cell line datasets and identified 423, 408, 386 and 361 variant peptides from BT474, MDMAB157, MFM223 and HCC38 datasets, respectively. Computational biology ; Genome ; Major histocompatibility complex ; Biology ; Gene ; Bioinformatics ; Computer science ; Genetics Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; RNA and protein synthesis mechanisms
Authors: Ibtissèm Gammoudi | Marion Mathelié‐Guinlet | Zeineb Benabdallah | Fabien Moroté | Houssem Kahli | Laure Béven | Rafik Kalfat | Ali Othmane | Marie‐Hélène Delville | Christine Grauby‐Heywang | Corinne Déjous | T. Cohen-Bouhacina
Source: Thin Solid Films (article, 2020-09-11)
Field: Materials Science — Surfaces, Coatings and Films

Revisiting of the physico-chemical properties of polyelectrolyte multilayers for a fine tuning of the immobilization of bacteria or nanoparticles Polyelectrolyte ; Materials science ; Nanotechnology ; Allylamine ; Chemical engineering ; Ionic strength ; Coating ; Polymer ; Substrate (aquarium) ; Layer by layer ; Nanoparticle ; Biofouling ; Deposition (geology) ; Chemistry ; Layer (electronics) ; Aqueous solution ; Membrane ; Organic chemistry ; Composite material Polymer Surface Interaction Studies ; Marine Biology and Environmental Chemistry ; Molecular Junctions and Nanostructures
Authors: Tomáš Urbánek | Jiří Trousil | Dmytro Rak | Kristýna Gunár | Rafał Konefał | Miroslav Šlouf | Marián Sedlák | Olga Janoušková | Martin Hrubý
Source: Macromolecular Bioscience (article, 2020-05-01)
Field: Materials Science — Biomaterials

γ‐Butyrolactone Copolymerization with the Well‐Documented Polymer Drug Carrier Poly(ethylene oxide)‐<i>block</i>‐poly(ε‐caprolactone) to Fine‐Tune Its Biorelevant Properties Front Cover: Copolymerization of γ-butyrolactone into ε-caprolactone-based block copolymers is proven to be an efficient tool to tailor biodegradation rate of nanoparticle drug delivery systems prepared from these copolymers. This monomeric unit accelerates biodegradation rate in a controlled manner. This is reported by Tomáš Urbánek, Jiří Trousil, Dmytro Rak, Kristýna Gunár, Rafał Konefał, Miroslav Šlouf, Marián Sedlák, Olga Šebestová Janoušková, Martin Hrubý in article 1900408. Copolymer ; Caprolactone ; Biodegradation ; Polymer chemistry ; Monomer ; Chemistry ; Ethylene oxide ; Drug delivery ; Polymer ; Organic chemistry biodegradable polymer synthesis and properties ; Biopolymer Synthesis and Applications
Authors: Guoqing Jin | Hao‐Zong Xue | Jun‐Long Zhang
Source: ChemPlusChem (review, 2020-08-02)
Field: Materials Science — Materials Chemistry

Porpholactone Chemistry: Shining New Light on an Old Cofactor The emergence of porpholactone chemistry, discovered over 30 years ago, has significantly stimulated the development of biomimetic tetrapyrrole chemistry. It offers an opportunity, through modifications of non-pyrrolic building blocks, to clarify the relationship between chemical structure and excited-state properties, deciphering the structural code for the biological functions of life pigments. With intriguing photophysical properties in the red to near-infrared (NIR) regions, facile modulation of their electronic nature by fine-tuning chemical structures, and coordination ability with diverse metal ions, these novel porphyrinoids have favorable prospects in the fields of optical materials, bioimaging and therapy, and catalysis. In this Minireview, we summarize the brief history of porpholactone chemistry, and focus on the studies carried out in our group, particularly on the regioisomeric effect, NIR lanthanide luminescence, and metal catalysis. We outline the perspectives of these compounds in the construction of porpholactone-related biomedical applications and optical and energy materials, in order to inspire more interest and further advance bioinspired inorganic chemistry and lanthanide chemical biology. Nanotechnology ; Lanthanide ; Chemistry ; Tetrapyrrole ; Materials science ; Organic chemistry ; Ion Porphyrin and Phthalocyanine Chemistry ; Molecular Sensors and Ion Detection ; Nanoplatforms for cancer theranostics
Authors: I.A. Solizoda | В.Е. Живулин | D. P. Sherstyuk | A.Yu. Starikov | Evgeny Trofimov | O.V. Zaitseva | Д.А. Винник
Source: Bulletin of the South Ural State University series Chemistry (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Synthesis and Structure of Ceramics of Bisubstituted M-Type Hexaferrite BaFe(11.5-x)Ti0.5AlxO19 The development of scientific and technological progress is impossible without the creation of new functional materials. One of the classes of such materials are hexagonal ferrites. Their unique physical properties make them an irreplaceable material for the production of high-frequency electronics. The widespread introduction of high-frequency electronics into everyday life, over the past decade, has generated great interest in hexagonal ferrites. The number of publications devoted to the synthesis of mono- and bisubstituted ferrites noticeably increases every year. Modification of the chemical composition of a ferrite by replacing some of the iron atoms with another element, without changing its structure, leads to a change in physical properties of the material. Variation of the final ferrite properties, by changing its chemical composition, is of interest and is promising for fine tuning the material properties for a specific task. The aim of the present work is to experimentally study the possibility of synthesizing ferrite with a magnetoplumbite structure, in which the iron atoms are partially replaced by the Al and Ti atoms. A review of the scientific literature on this issue showed the absence of publications on ferrites with such a set of substitute elements. The X-ray phase and structural analysis, electron microscopy, and energy-dispersive X-ray spectroscopy were used as research methods in the present study. The article offers the results of an experimental study of the possibility of obtaining bisubstituted M-type ferrite of the BaFe(11.5-x)Ti0.5AlxO19 composition, where x (Al) = 0.1, 0.5, 1. Solid-phase synthesis has been used as a method for preparing samples. This method is devoid of technological difficulties and is promising from the point of view of its scaling for the synthesis of ferrite. The samples have been sintered at three different temperatures: 1300, 1350, and 1400 °C. It is shown that in the temperature range 1300–1400 ° C the formation of monophase samples occurs. The calculation of the parameters of the crystal lattice has been made. The influence of temperature and concentration of a substituting element on the change in the parameters of the crystal lattice of the material has been revealed. The study by the electron microscopy method made it possible to reveal the presence of latent microporosity of the samples. Ferrite (magnet) ; Hexagonal crystal system ; Ceramic ; Materials science ; Crystal structure ; Engineering physics ; Crystallography ; Nanotechnology ; Metallurgy ; Chemistry ; Composite material ; Physics Magnetic Properties and Synthesis of Ferrites ; Bauxite Residue and Utilization ; Pigment Synthesis and Properties
Authors: Dmytro Antypov | Argyrios Deligkas | Vladimir V. Gusev | Matthew J. Rosseinsky | Paul G. Spirakis | Michail Theofilatos
Source: DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) (preprint, 2020-01-01)
Field: Materials Science — Materials Chemistry

Crystal Structure Prediction via Oblivious Local Search We study Crystal Structure Prediction, one of the major problems in computational chemistry. This is essentially a continuous optimization problem, where many different, simple and sophisticated, methods have been proposed and applied. The simple searching techniques are easy to understand, usually easy to implement, but they can be slow in practice. On the other hand, the more sophisticated approaches perform well in general, however almost all of them have a large number of parameters that require fine tuning and, in the majority of the cases, chemical expertise is needed in order to properly set them up. In addition, due to the chemical expertise involved in the parameter-tuning, these approaches can be biased towards previously-known crystal structures. Our contribution is twofold. Firstly, we formalize the Crystal Structure Prediction problem, alongside several other intermediate problems, from a theoretical computer science perspective. Secondly, we propose an oblivious algorithm for Crystal Structure Prediction that is based on local search. Oblivious means that our algorithm requires minimal knowledge about the composition we are trying to compute a crystal structure for. In addition, our algorithm can be used as an intermediate step by any method. Our experiments show that our algorithms outperform the standard basin hopping, a well studied algorithm for the problem. Crystal structure prediction ; Simple (philosophy) ; Computer science ; Set (abstract data type) ; Algorithm ; Crystal (programming language) ; Perspective (graphical) ; Order (exchange) ; Crystal structure ; Theoretical computer science ; Artificial intelligence ; Chemistry ; Crystallography Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Analytical Chemistry and Chromatography
Authors: Yanli Ding | Tonghui Yang | Naiqiang Yin | Peng Li | Ying Zhao | Xiaodan Zhang
Source: ScienceAsia (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Yb3+/Er3+ concentration dependent microstructure evolution and green/red emissions of NaYF4:Yb/Er phosphors Photon upconversion is promising for applications such as data storage, drug delivery and solar cells. -NaYF 4 :Yb/Er samples were synthesized by a facile hydrothermal method. The effects of Yb/Er ratio on the microstructures, morphology evolution and luminescence properties were studied. The SEM results showed that the morphology of the samples evolved gradually from plate to prismatic structure with an increase in Yb 3+ concentration. This indicates that the growth rate along the c-axis crystal planes of NaYbF 4 lattices is more rapid than NaYF 4 lattices. Photoluminescence measurements demonstrate that the bright multicolored upconversion emissions can be fine-tuned from green to red by adjusting the codoped Yb/Er ratio under 980 nm laser excitation. The tunable emission is due to the energy back transfer from Yb 3+ to Er 3+ . Applying this material in perovskite solar cell, a current density of 4 A cm -2 is obtained under 40 mW and 980 nm laser excitation. Phosphor ; Microstructure ; Materials science ; Chemistry ; Chemical engineering ; Metallurgy ; Optoelectronics Luminescence Properties of Advanced Materials ; Radiation Detection and Scintillator Technologies ; Inorganic Fluorides and Related Compounds