jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Gaozhen Liang | Chunwang Dong | Bin Hu | Hongkai Zhu | Haibo Yuan | Yongwen Jiang | Guoshuang Hao
Source: Scientific Reports (article, 2018-05-14)
Field: Chemistry — Analytical Chemistry

Prediction of Moisture Content for Congou Black Tea Withering Leaves Using Image Features and Nonlinear Method Withering is the first step in the processing of congou black tea. With respect to the deficiency of traditional water content detection methods, a machine vision based NDT (Non Destructive Testing) method was established to detect the moisture content of withered leaves. First, according to the time sequences using computer visual system collected visible light images of tea leaf surfaces, and color and texture characteristics are extracted through the spatial changes of colors. Then quantitative prediction models for moisture content detection of withered tea leaves was established through linear PLS (Partial Least Squares) and non-linear SVM (Support Vector Machine). The results showed correlation coefficients higher than 0.8 between the water contents and green component mean value (G), lightness component mean value (L<sup>*</sup>) and uniformity (U), which means that the extracted characteristics have great potential to predict the water contents. The performance parameters as correlation coefficient of prediction set (Rp), root-mean-square error of prediction (RMSEP), and relative standard deviation (RPD) of the SVM prediction model are 0.9314, 0.0411 and 1.8004, respectively. The non-linear modeling method can better describe the quantitative analytical relations between the image and water content. With superior generalization and robustness, the method would provide a new train of thought and theoretical basis for the online water content monitoring technology of automated production of black tea. Water content ; Black tea ; Nonlinear system ; Image (mathematics) ; Content (measure theory) ; Botany ; Computer science ; Biological system ; Horticulture ; Environmental science ; Mathematics ; Biology ; Artificial intelligence ; Food science ; Geology ; Physics ; Mathematical analysis Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Tea Polyphenols and Effects
Authors: Yu Chen | Yanli Ma | Weipeng Lu | Yanchuan Guo | Yi Zhu | Haojun Lu | Yeping Song
Source: Molecules (article, 2018-09-27)
Field: Materials Science — Biomaterials

Environmentally Friendly Gelatin/β-Cyclodextrin Composite Fiber Adsorbents for the Efficient Removal of Dyes from Wastewater In this paper, environmentally friendly gelatin/<i>β</i>-cyclodextrin (<i>β</i>-CD) composite fiber adsorbents prepared by electrospinning were used for the removal of dyes from wastewater. Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and a universal materials tester were employed to characterize the internal structures, surface morphologies and mechanical strength of the composite fiber adsorbents. Additionally, the fiber was evaluated as an adsorbent for the removal of methylene blue (MB) from aqueous solution. The effects of the raw material ratio, pH, temperature, concentration and adsorption time were studied. The results show that the gelatin/<i>β</i>-CD composite fiber adsorbents possess excellent mechanical strength and high adsorption efficiency for MB. The adsorption equilibrium and adsorption kinetics are well-described by the Langmuir isotherm model and the pseudo-second-order kinetic model, respectively. The theoretical maximum adsorption capacity is 47.4 mg·g<sup>-1</sup>. Additionally, after nine successive desorption-adsorption cycles, the removal rate is still over 70%. Moreover, the gelatin/<i>β</i>-CD composite fiber adsorbents exhibit excellent adsorption capability for basic fuchsin, gentian violet, brilliant blue R and malachite green dyes. Therefore, owing to the characteristics of degradability, low cost and high-efficiency, the gelatin/<i>β</i>-CD composite fiber can be used as an efficient adsorbent for the removal of dyes from wastewater. Adsorption ; Gelatin ; Langmuir adsorption model ; Malachite green ; Fiber ; Composite number ; Chemical engineering ; Fourier transform infrared spectroscopy ; Aqueous solution ; Electrospinning ; Materials science ; Methylene blue ; Desorption ; Nuclear chemistry ; Crystal violet ; Chemistry ; Composite material ; Organic chemistry ; Polymer Electrospun Nanofibers in Biomedical Applications ; Graphene and Nanomaterials Applications ; Adsorption and biosorption for pollutant removal
Authors: Tiannan Guo | Li Li | Qing Zhong | Niels J. Rupp | Konstantina Charmpi | Christine E. Wong | Ulrich Wagner | Jan H. Rueschoff | Wolfram Jochum | Christian D. Fankhauser | Karim Saba | Cédric Poyet | Peter J. Wild | Ruedi Aebersold | Andreas Beyer
Source: Life Science Alliance (article, 2018-05-01)
Field: Chemistry — Spectroscopy

Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers It remains unclear to what extent tumor heterogeneity impacts on protein biomarker discovery. Here, we quantified proteome intra-tissue heterogeneity (ITH) based on a multi-region analysis of prostate tissues using pressure cycling technology and SWATH mass spectrometry. We quantified 6,873 proteins and analyzed the ITH of 3,700 proteins. The level of ITH varied depending on proteins and tissue types. Benign tissues exhibited more complex ITH patterns than malignant tissues. Spatial variability of ten prostate biomarkers was validated by immunohistochemistry in an independent cohort (n=83) using tissue microarrays. PSA was preferentially variable in benign prostatic hyperplasia, while GDF15 substantially varied in prostate adenocarcinomas. Further, we found that DNA repair pathways exhibited a high degree of variability in tumorous tissues, which may contribute to the genetic heterogeneity of tumors. This study conceptually adds a new perspective to protein biomarker discovery: it suggests that recent technological progress should be exploited to quantify and account for spatial proteome variation to complement biomarker identification and utilization. Biomarker discovery ; Proteome ; Biomarker ; Prostate ; Prostate cancer ; Tissue microarray ; Computational biology ; Proteomics ; Biology ; Hyperplasia ; Pathology ; Immunohistochemistry ; Bioinformatics ; Medicine ; Cancer ; Genetics Advanced Proteomics Techniques and Applications ; Prostate Cancer Treatment and Research ; Molecular Biology Techniques and Applications
Authors: Xian Kong | Junkai Deng | Lou Li | Yilun Liu | Xiangdong Ding | Jun Sun | Jefferson Zhe Liu
Source: Physical review. B./Physical review. B (article, 2018-11-16)
Field: Materials Science — Materials Chemistry

Tunable auxetic properties in group-IV monochalcogenide monolayers Negative Poisson's ratio (NPR) is a counterintuitive material elastic constant that can lead to many unusual auxetic properties. Here, using first-principles calculations, we report tunable negative Poisson's ratio in the out-of-plane direction in group-IV monochalcogenide monolayers $MX$ ($M=\text{Sn}$, Ge and $X=\text{S}$, Se). SnSe, GeS, and SnS monolayers have intrinsic NPR ${\ensuremath{\nu}}_{zx}$ ranging from $\ensuremath{-}0.004$ to $\ensuremath{-}0.210$ in armchair ($x$) tension, whereas GeSe monolayer possesses a much larger NPR ${\ensuremath{\nu}}_{zy}$ of $\ensuremath{-}0.433$ in zigzag ($y$) tension. Our analysis attributes the NPR effects to the relative position of $M$ and $X$ in the puckered structure and the smaller bending stiffness of $M\text{\ensuremath{-}}X\text{\ensuremath{-}}M$ bond angle. We further established the correlation between electronic structures of materials and their crystal structures. It allows us to fine tune GeSe structure via electron doping, leading to a reversible and continuous change of ${\ensuremath{\nu}}_{zy}$ from $\ensuremath{-}0.821$ up to 0.895. We also demonstrate the concept of strain engineering GeSe monolayer to switch its Poisson's ratio ${\ensuremath{\nu}}_{zx}$ between two different values: 0.583 and $\ensuremath{-}0.433$. Our in-depth study provides not only fundamental knowledge but also practical routes for designing 2D smart materials with tunable negative Poisson's ratio, which are desirable for smart devices at small scale. Auxetics ; Monolayer ; Zigzag ; Poisson's ratio ; Condensed matter physics ; Materials science ; Crystallography ; Bending stiffness ; Physics ; Poisson distribution ; Bending ; Nanotechnology ; Geometry ; Composite material ; Mathematics ; Chemistry 2D Materials and Applications ; MXene and MAX Phase Materials ; Cellular and Composite Structures
Authors: Gonela Vijaykumar | Anand Pariyar | Jasimuddin Ahmed | Bikash Kumar Shaw | Debashis Adhikari | Swadhin K. Mandal
Source: Chemical Science (article, 2018-01-01)
Field: Chemistry — Organic Chemistry

Tuning the redox non-innocence of a phenalenyl ligand toward efficient nickel-assisted catalytic hydrosilylation In this report, a ligand-redox assisted catalytic hydrosilylation has been investigated. A phenalenyl ligand coordinated nickel complex has been utilized as an electron reservoir to develop a base metal-assisted catalyst, which very efficiently hydrosilylates a wide variety of olefin substrates under ambient conditions. A mechanistic investigation revealed that a two-electron reduced phenalenyl based biradical nickel complex plays the key role in such catalysis. The electronic structure of the catalytically active biradical species has been interrogated using EPR spectroscopy, magnetic susceptibility measurements, and electronic structure calculations using a DFT method. Inhibition of the reaction by a radical quencher, as well as the mass spectrometric detection of two intermediates along the catalytic loop, suggest that a single electron transfer from the ligand backbone initiates the catalysis. The strategy of utilising the redox reservoir property of the ligand ensures that the nickel is not promoted to an unfavorable oxidation state, and the fine tuning between the ligand and metal redox orbitals elicits smooth catalysis. Hydrosilylation ; Nickel ; Redox ; Catalysis ; Ligand (biochemistry) ; Chemistry ; Photochemistry ; Combinatorial chemistry ; Polymer chemistry ; Organic chemistry Organoboron and organosilicon chemistry ; Organometallic Complex Synthesis and Catalysis ; N-Heterocyclic Carbenes in Organic and Inorganic Chemistry
Authors: Jana Broecker | Takefumi Morizumi | Wei‐Lin Ou | Viviane Klingel | Anling Kuo | David J. Kissick | Andrii Ishchenko | Ming-Yue Lee | Shenglan Xu | О. А. Макаров | Vadim Cherezov | Craig M. Ogata | Oliver P. Ernst
Source: Nature Protocols (article, 2018-01-04)
Field: Materials Science — Materials Chemistry

High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions Protein crystallization ; In situ ; Crystallization ; Materials science ; Membrane ; Nanotechnology ; Chemical engineering ; Chemistry Enzyme Structure and Function ; Protein Structure and Dynamics ; Advanced Proteomics Techniques and Applications
Authors: Atsuto Seko | Hiroyuki Hayashi | Hisashi Kashima | Isao Tanaka
Source: Physical Review Materials (article, 2018-01-16)
Field: Materials Science — Materials Chemistry

Matrix- and tensor-based recommender systems for the discovery of currently unknown inorganic compounds Chemically relevant compositions (CRCs) and atomic arrangements of inorganic compounds have been collected as inorganic crystal structure databases. Machine learning is a unique approach to search for currently unknown CRCs from vast candidates. Herein we propose matrix- and tensor-based recommender system approaches to predict currently unknown CRCs from database entries of CRCs. Firstly, the performance of the recommender system approaches to discover currently unknown CRCs is examined. A Tucker decomposition recommender system shows the best discovery rate of CRCs as the majority of the top 100 recommended ternary and quaternary compositions correspond to CRCs. Secondly, systematic density functional theory (DFT) calculations are performed to investigate the phase stability of the recommended compositions. The phase stability of the 27 compositions reveals that 23 currently unknown compounds are newly found to be stable. These results indicate that the recommender system has great potential to accelerate the discovery of new compounds. Recommender system ; Matrix (chemical analysis) ; Computer science ; Tensor (intrinsic definition) ; Data science ; Information retrieval ; Chemistry ; Mathematics ; Chromatography ; Pure mathematics Machine Learning in Materials Science ; Zeolite Catalysis and Synthesis ; Advanced NMR Techniques and Applications
Authors: Andrew W. Knight | A Tigges | Anastasia Ilgen
Source: Geochemical Transactions (article, 2018-06-26)
Field: Materials Science — Materials Chemistry

Adsorption of copper (II) on mesoporous silica: the effect of nano-scale confinement Nano-scale spatial confinement can alter chemistry at mineral-water interfaces. These nano-scale confinement effects can lead to anomalous fate and transport behavior of aqueous metal species. When a fluid resides in a nanoporous environments (pore size under 100 nm), the observed density, surface tension, and dielectric constant diverge from those measured in the bulk. To evaluate the impact of nano-scale confinement on the adsorption of copper (Cu<sup>2+</sup>), we performed batch adsorption studies using mesoporous silica. Mesoporous silica with the narrow distribution of pore diameters (SBA-15; 8, 6, and 4 nm pore diameters) was chosen since the silanol functional groups are typical to surface environments. Batch adsorption isotherms were fit with adsorption models (Langmuir, Freundlich, and Dubinin-Radushkevich) and adsorption kinetic data were fit to a pseudo-first-order reaction model. We found that with decreasing pore size, the maximum surface area-normalized uptake of Cu<sup>2+</sup> increased. The pseudo-first-order kinetic model demonstrates that the adsorption is faster as the pore size decreases from 8 to 4 nm. We attribute these effects to the deviations in fundamental water properties as pore diameter decreases. In particular, these effects are most notable in SBA-15 with a 4-nm pore where the changes in water properties may be responsible for the enhanced Cu mobility, and therefore, faster Cu adsorption kinetics. Adsorption ; Silanol ; Langmuir ; Mesoporous material ; Copper ; Nanoporous ; Mesoporous silica ; Aqueous solution ; Chemical engineering ; Freundlich equation ; Materials science ; Sorption ; Chemistry ; Nanotechnology ; Physical chemistry ; Organic chemistry ; Catalysis ; Metallurgy Mesoporous Materials and Catalysis ; Iron oxide chemistry and applications ; Electrostatics and Colloid Interactions
Authors: Karthikeyan Sekar | Santosh Kumar | Lee J. Durndell | Mark A. Isaacs | Christopher M. A. Parlett | Ben A. Coulson | R.E. Douthwaite | Zhi Jiang | Karen Wilson | Adam F. Lee
Source: ChemCatChem (article, 2018-06-15)
Field: Materials Science — Materials Chemistry

Size‐Dependent Visible Light Photocatalytic Performance of Cu<sub>2</sub>O Nanocubes Abstract Well‐defined Cu 2 O nanocubes with tunable dimensions and physicochemical properties have been prepared using a simple one‐pot reaction. Reduction of Cu(II) salts by ascorbic acid in the presence of PEG as a structure‐directing agent affords crystalline Cu 2 O nanocubes of between 50 to 500 nm. Optical band gap, band energies, charge‐carrier lifetimes and surface oxidation state systematically evolve with nanocube size, and correlate well with visible light photocatalytic activity for aqueous phase phenol degradation and H 2 production which are both directly proportional to size (doubling between 50 and 500 nm). HPLC reveals fumaric acid as the primary organic product of phenol degradation, and selectivity increases with nanocube size at the expense of toxic catechol. Apparent quantum efficiencies reach 26 % for phenol photodegradation and 1.2 % for H 2 production using 500 nm Cu 2 O cubes. Photocatalysis ; Photodegradation ; Phenol ; Visible spectrum ; Ascorbic acid ; Selectivity ; Photochemistry ; Aqueous solution ; Band gap ; Chemistry ; Materials science ; Catechol ; Catalysis ; Organic chemistry Copper-based nanomaterials and applications ; Advanced Photocatalysis Techniques ; ZnO doping and properties
Authors: Arka Mukhopadhyay | Sankar Basu | Santiswarup Singha | Hirak K. Patra
Source: Research (review, 2018-01-01)
Field: Materials Science — Biomaterials

Inner-View of Nanomaterial Incited Protein Conformational Changes: Insights into Designable Interaction Nanoparticle bioreactivity critically depends upon interaction between proteins and nanomaterials (NM). The formation of the "protein corona" (PC) is the effect of such nanoprotein interactions. PC has a wide usage in pharmaceuticals, drug delivery, medicine, and industrial biotechnology. Therefore, a detailed in-vitro, in-vivo, and in-silico understanding of nanoprotein interaction is fundamental and has a genuine contemporary appeal. NM surfaces can modify the protein conformation during interaction, or NMs themselves can lead to self-aggregations. Both phenomena can change the whole downstream bioreactivity of the concerned nanosystem. The main aim of this review is to understand the mechanistic view of NM-protein interaction and recapitulate the underlying physical chemistry behind the formation of such complicated macromolecular assemblies, to provide a critical overview of the different models describing NM induced structural and functional modification of proteins. The review also attempts to point out the current limitation in understanding the field and highlights the future scopes, involving a plausible proposition of how artificial intelligence could be aided to explore such systems for the prediction and directed design of the desired NM-protein interactions. Nanotechnology ; In silico ; Protein–protein interaction ; Chemistry ; Nanomaterials ; Biophysics ; Computational biology ; Computer science ; Materials science ; Biology ; Biochemistry Nanoparticle-Based Drug Delivery ; Enzyme Production and Characterization ; Polymer Surface Interaction Studies
Authors: Boone M. Prentice | Daniel J. Ryan | Raf Van de Plas | Richard M. Caprioli | Jeffrey M. Spraggins
Source: Analytical Chemistry (article, 2018-02-14)
Field: Chemistry — Spectroscopy

Enhanced Ion Transmission Efficiency up to <i>m</i>/<i>z</i> 24 000 for MALDI Protein Imaging Mass Spectrometry The molecular identification of species of interest is an important part of an imaging mass spectrometry (IMS) experiment. The high resolution accurate mass capabilities of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) have recently been shown to facilitate the identification of proteins in matrix-assisted laser desorption/ionization (MALDI) IMS. However, these experiments are typically limited to proteins giving rise to ions of relatively low m/ z due to difficulties transmitting and measuring large molecular weight ions of low charge states. Herein we have modified the source gas manifold of a commercial MALDI FT-ICR MS to regulate the gas flow and pressure to maximize the transmission of large m/ z protein ions through the ion funnel region of the instrument. By minimizing the contribution of off-axis gas disruption to ion focusing and maximizing the effective potential wall confining the ions through pressure optimization, the signal-to-noise ratios (S/N) of most protein species were improved by roughly 1 order of magnitude compared to normal source conditions. These modifications enabled the detection of protein standards up to m/ z 24 000 and the detection of proteins from tissue up to m/ z 22 000 with good S/N, roughly doubling the mass range for which high quality protein ion images from rat brain and kidney tissue could be produced. Due to the long time-domain transients (>4 s) required to isotopically resolve high m/ z proteins, we have used these data as part of an FT-ICR IMS-microscopy data-driven image fusion workflow to produce estimated protein images with both high mass and high spatial resolutions. Chemistry ; Mass spectrometry ; Mass spectrometry imaging ; MALDI imaging ; Ion ; Ion-mobility spectrometry ; Matrix-assisted laser desorption/ionization ; Analytical Chemistry (journal) ; Chromatography ; Organic chemistry Mass Spectrometry Techniques and Applications ; Ion-surface interactions and analysis ; Advanced Proteomics Techniques and Applications
Authors: Juan Sánchez-Weatherby | James Sandy | Halina Mikolajek | Carina M. C. Lobley | Marco Mazzorana | Jon Kelly | G. Preece | Rich Littlewood | Thomas Sørensen
Source: Journal of Synchrotron Radiation (article, 2018-11-23)
Field: Materials Science — Materials Chemistry

VMXi: a fully automated, fully remote, high-flux <i>in situ</i> macromolecular crystallography beamline VMXi is a new high-flux microfocus macromolecular crystallography beamline at Diamond Light Source. The beamline, dedicated to fully automated and fully remote data collection of macromolecular crystals in situ, allows rapid screening of hundreds of crystallization plates from multiple user groups. Its main purpose is to give fast feedback at the complex stages of crystallization and crystal optimization, but it also enables data collection of small and delicate samples that are particularly difficult to harvest using conventional cryo-methods, crystals grown in the lipidic cubic phase, and allows for multi-crystal data collections in drug discovery programs. The beamline is equipped with two monochromators: one with a narrow band-pass and fine energy resolution (optimal for regular oscillation experiments), and one with a wide band-pass and a high photon flux (optimal for fast screening). The beamline has a state-of-the-art detector and custom goniometry that allows fast data collection. This paper describes the beamline design, current status and future plans. Beamline ; Optics ; Detector ; Crystal (programming language) ; Crystallization ; Materials science ; Diamond ; Synchrotron ; Goniometer ; Physics ; Computer science Enzyme Structure and Function ; Advanced Fluorescence Microscopy Techniques ; Mass Spectrometry Techniques and Applications
Authors: Adam M. Wojciechowski | Mürsel Karadas | Christian Osterkamp | Steffen Jankuhn | Jan Meijer | Fedor Jelezko | Alexander Huck | Ulrik L. Andersen
Source: Applied Physics Letters (article, 2018-07-02)
Field: Materials Science — Materials Chemistry

Precision temperature sensing in the presence of magnetic field noise and <i>vice-versa</i> using nitrogen-vacancy centers in diamond We demonstrate a technique for precision sensing of the temperature or the magnetic field by simultaneously driving two hyperfine transitions involving distinct electronic states of the nitrogen-vacancy center in diamond. Frequency modulation of both driving fields is used with either the same or opposite phase, resulting in the immunity to fluctuations in either the magnetic field or the temperature, respectively. In this way, a sensitivity of 1.4 nT Hz−1∕2 or 430 μK Hz−1∕2 is demonstrated. The presented technique only requires a single frequency demodulator and enables the use of phase-sensitive camera imaging sensors. A simple extension of the method utilizing two demodulators allows for simultaneous, independent, and high-bandwidth monitoring of both the magnetic field and the temperature. Diamond ; Demodulation ; Magnetic field ; Hyperfine structure ; Temperature measurement ; Vacancy defect ; Bandwidth (computing) ; Physics ; Materials science ; Condensed matter physics ; Nuclear magnetic resonance ; Optoelectronics ; Atomic physics ; Computer science ; Telecommunications Diamond and Carbon-based Materials Research ; High-pressure geophysics and materials ; Force Microscopy Techniques and Applications