jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Zhaolian Lu | Yingjian Chen | Xin-yan Jing | Nana Wang | Ting Zhang | Chengjin Hu
Source: Medical Science Monitor (article, 2018-03-17)
Field: Chemistry — Spectroscopy

Detection and Identification of Serum Peptides Biomarker in Papillary Thyroid Cancer BACKGROUND Papillary thyroid cancer (PTC) is currently the most commonly diagnosed endocrine malignancy. In addition, the sex- and age-adjusted incidence of PTC has exhibited a greater increase over the last 2 decades than in many other malignancies. Thus, discovering noninvasive specific serum biomarker to distinguish PTC from cancer-free controls in its early stages remains an important goal. MATERIAL AND METHODS Serum samples from 88 PTC patients and 80 cancer-free controls were randomly allocated into training or validation sets. Serum peptide profiling was performed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) after using weak cation exchange magnetic beads (WCX-MB), and the results were evaluated by use of ClinProTools™ Software. To distinguish PTC from cancer-free controls, quick classifier (QC), supervised neural network (SNN), and genetic algorithm (GA) models were established. The models were blindly validated to verify their diagnostic capabilities. The most discriminative peaks were subsequently identified with a nano-liquid chromatography-electrospray ionization-tandem mass spectrometry system. RESULTS Six peptide ions were identified as the most discriminative peaks between the PTC and cancer-free control samples. The QC model exhibited satisfactory sensitivity and specificity among the 3 models that were validated. Two peaks, at m/z 2671.17 and m/z 1464.68, were identified as fragments of the alpha chain of fibrinogen, while a peak at m/z 1738.92 was a fragment of complement component 4A/B. CONCLUSIONS MS combined with ClinProTools™ software was able to detect peptide biomarkers in PTC patients. In addition, the constructed classification models provided a serum peptidome pattern for distinguishing PTC from cancer-free controls. Both fibrinogen a and complement C4A/B were identified as potential markers for diagnosis of PTC. Thyroid cancer ; Papillary thyroid cancer ; Biomarker ; Electrospray ionization ; Mass spectrometry ; Medicine ; Cancer ; Tandem mass spectrometry ; Internal medicine ; Chromatography ; Chemistry ; Biochemistry Advanced Proteomics Techniques and Applications ; Thyroid Cancer Diagnosis and Treatment ; Machine Learning in Bioinformatics
Authors: Chong Qiao | Yixuan Guo | Jing-Kai Wang | Hong Shen | Songyou Wang | Yu-Xiang Zheng | R.J. Zhang | L.Y. Chen | C.Z. Wang | Kai‐Ming Ho
Source: Journal of Alloys and Compounds (article, 2018-10-03)
Field: Materials Science — Materials Chemistry

The local structural differences in amorphous Ge-Sb-Te alloys Chalcogenide ; Amorphous solid ; Octahedron ; Materials science ; Crystallography ; Tetrahedron ; Cluster (spacecraft) ; Alloy ; Atom (system on chip) ; Chemical physics ; Phase (matter) ; Molecular dynamics ; Condensed matter physics ; Nanotechnology ; Crystal structure ; Chemistry ; Computational chemistry ; Physics ; Optoelectronics ; Metallurgy Phase-change materials and chalcogenides ; Chalcogenide Semiconductor Thin Films ; Crystal Structures and Properties
Authors: Chih-Kai Chang | Hui-Min Wang | John Chi‐Wei Lan
Source: Polymers (article, 2018-03-22)
Field: Materials Science — Biomaterials

Investigation and Characterization of Plasma-Treated Poly(3-hydroxybutyrate) and Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Biopolymers for an In Vitro Cellular Study of Mouse Adipose-Derived Stem Cells Polyhydroxyalkanoates (PHAs) are a type of thermoprocessable and biodegradable polyester, which represent a potential sustainable replacement for fossil-fuel synthetic polymers, such as polypropylene and polyethylene. In recent years, copolymers of PHAs, i.e., poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-<i>co</i>-3-hydroxyvalerate) (PHBV), have received attention for medical and packaging industrial applications, due to their biodegradable, toxic-free, and biocompatible nature. This study investigated and characterized plasma-treated PHB and PHBV films fermented with <i>Ralstonia eutropha</i> H16. The X-ray photoelectron spectroscopy (XPS) and water contact angle analyses on the plasma-treated PHB and PHBV film surfaces revealed an increase in the number of functional groups and contact angle degree, respectively, compared to that of the untreated films. In addition, an in vitro experiment of mouse adipose-derived stem cells showed better growth and adhesion of the cells on the surface of plasma-treated PHBV film. Overall, these results reveal that plasma surface modifications are useful in biomaterial development. Polyhydroxyalkanoates ; Contact angle ; Polyester ; Materials science ; Biomaterial ; Adhesion ; X-ray photoelectron spectroscopy ; Biodegradable polymer ; Chemical engineering ; Polymer chemistry ; Surface modification ; Polymer ; In vitro ; Polyethylene ; Chemistry ; Biochemistry ; Composite material ; Nanotechnology ; Bacteria biodegradable polymer synthesis and properties ; Additive Manufacturing and 3D Printing Technologies ; Electrospun Nanofibers in Biomedical Applications
Authors: Edwin R. Arboleda
Source: International Journal of Advanced Computer Research (article, 2018-11-30)
Field: Chemistry — Analytical Chemistry

Discrimination of civet coffee using near infrared spectroscopy and artificial neural network Civet coffee refers to the coffee that includes partlydigested coffee cherries eaten and defecated by the palm civet cat (Paradoxurus hermaphrodites). Civet cats seek out and eat only the ripest, reddish coffee cherries. The coffee cherry fruit is sweet and is completely digested, but the beans are excreted in their feces. It is one of the rarest and priciest coffees in the world At present, there is still no accepted standard in determining the authenticity of the civet coffee Due to its high price, the traditional method of collecting feces from the wild civets has given way to a farming method where civets are kept in cages and force-fed with the cherries. Most of the previous studies done in discriminating civet coffee from ordinary coffee beans used a destructive method of sampling, preparation wherein coffee beans were grounded and results can take a very long time. The forte of the NIRS technique lies in its speed Artificial neural network ; Artificial intelligence ; Computer science Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Coffee research and impacts
Authors: Guo Zhao | Hui Wang | Gang Liu
Source: RSC Advances (article, 2018-01-01)
Field: Chemistry — Electrochemistry

Sensitive determination of trace Cd(<scp>ii</scp>) and Pb(<scp>ii</scp>) in soil by an improved stripping voltammetry method using two different<i>in situ</i>plated bismuth-film electrodes based on a novel electrochemical measurement system In this study, a simple but effective electrochemical method was developed to minimize the interference from real soil samples and increase the sensitivity of Pb(ii) and Cd(ii) detection by square-wave anodic stripping voltammetry (SWASV) using a novel electrochemical measurement system, which can be used for the on-site determination of trace Cd(ii) and Pb(ii) in real soil samples. The method involved performing SWASV following double deposition and stripping steps at two <i>in situ</i> plated bismuth-film electrodes with drastically different surface properties. Pb(ii) and Cd(ii) were first deposited on an <i>in situ</i> plated bismuth-film graphite carbon paste electrode (Bi/GCPE). When the first deposition was finished, the GCPE was moved to a micro-electrolytic cell to perform the first stripping step. The following measurements were performed with the other deposition and stripping steps using a highly sensitive <i>in situ</i> plated bismuth-film multiwalled carbon nanotube-Nafion composite modified glassy carbon electrode (Bi/MWCNT-Nafion/GCE) as the working electrode. Pb(ii), Cd(ii) and Bi(iii) stripped from the GCPE in the micro-electrolytic cell were partially deposited on the MWCNT-Nafion/GCE, and the stripping current signals were obtained from their oxidation during the second stripping step. Considering the small volume of the micro-electrolytic cell, the concentrations of Cd(ii) and Pb(ii) were drastically higher than those in the bulk solution, and therefore, the detection limits were reduced. Under the optimized conditions, the concentrations in the linear range spanned from 1.0 to 45.0 μg L<sup>-1</sup> for both Pb(ii) and Cd(ii), with a detection limit of 0.03 μg L<sup>-1</sup> for Pb(ii) and 0.02 μg L<sup>-1</sup> for Cd(ii) (S/N = 3). Finally, analyses of real samples were performed to detect trace levels of Pb(ii) and Cd(ii) in soil with satisfactory results. Bismuth ; Anodic stripping voltammetry ; Stripping (fiber) ; Nafion ; Electrode ; Analytical Chemistry (journal) ; Materials science ; Working electrode ; Electrolyte ; Electrochemistry ; Supporting electrolyte ; Chemistry ; Chromatography ; Composite material ; Metallurgy Electrochemical Analysis and Applications ; Analytical Chemistry and Sensors ; Electrochemical sensors and biosensors
Authors: Daniela Hulcová | Kateřina Breiterová | Tomáš Siatka | Kamila Klímová | Lara Davani | Marcela Šafratová | Anna Hošťálková | Angela De Simone | Vincenza Andrisano | Lucie Cahlíková
Source: Molecules (article, 2018-03-21)
Field: Chemistry — Organic Chemistry

Amaryllidaceae Alkaloids as Potential Glycogen Synthase Kinase-3β Inhibitors Glycogen synthase kinase-3β (GSK-3β) is a multifunctional serine/threonine protein kinase that was originally identified as an enzyme involved in the control of glycogen metabolism. It plays a key role in diverse physiological processes including metabolism, the cell cycle, and gene expression by regulating a wide variety of well-known substances like glycogen synthase, tau-protein, and β-catenin. Recent studies have identified GSK-3β as a potential therapeutic target in Alzheimer´s disease, bipolar disorder, stroke, more than 15 types of cancer, and diabetes. GSK-3β is one of the most attractive targets for medicinal chemists in the discovery, design, and synthesis of new selective potent inhibitors. In the current study, twenty-eight Amaryllidaceae alkaloids of various structural types were studied for their potency to inhibit GSK-3β. Promising results have been demonstrated by alkaloids of the homolycorine-{9-<i>O</i>-demethylhomolycorine (IC<sub>50</sub> = 30.00 ± 0.71 µM), masonine (IC<sub>50</sub> = 27.81 ± 0.01 μM)}, and lycorine-types {caranine (IC<sub>50</sub> = 30.75 ± 0.04 μM)}. GSK-3 ; Amaryllidaceae Alkaloids ; Glycogen synthase ; Biochemistry ; GSK3B ; Kinase ; Enzyme ; Biology ; Protein kinase A ; Chemistry ; Alkaloid ; Stereochemistry Chemical synthesis and alkaloids ; Alkaloids: synthesis and pharmacology ; Cholinesterase and Neurodegenerative Diseases
Authors: Jinnuo Zhang | Xuping Feng | Xiaodan Liu | Yong He
Source: Applied Sciences (article, 2018-10-01)
Field: Chemistry — Analytical Chemistry

Identification of Hybrid Okra Seeds Based on Near-Infrared Hyperspectral Imaging Technology Near-infrared (874–1734 nm) hyperspectral imaging technology combined with chemometrics was used to identify parental and hybrid okra seeds. A total of 1740 okra seeds of three different varieties, which contained the male parent xiaolusi, the female parent xianzhi, and the hybrid seed penzai, were collected, and all of the samples were randomly divided into the calibration set and the prediction set in a ratio of 2:1. Principal component analysis (PCA) was applied to explore the separability of different seeds based on the spectral characteristics of okra seeds. Fourteen and 86 characteristic wavelengths were extracted by using the successive projection algorithm (SPA) and competitive adaptive reweighted sampling (CARS), respectively. Another 14 characteristic wavelengths were extracted by using CARS combined with SPA. Partial least squares discriminant analysis (PLS-DA) and support vector machine (SVM) were developed based on the characteristic wavelength and full-band spectroscopy. The experimental results showed that the SVM discriminant model worked well and that the correct recognition rate was over 93.62% based on full-band spectroscopy. As for the discriminative model that was based on characteristic wavelength, the SVM model based on the CARS algorithm was better than the other two models. Combining the CARS+SVM calibration model and image processing technology, a pseudo-color map of sample prediction was generated, which could intuitively identify the species of okra seeds. The whole process provided a new idea for agricultural breeding in the rapid screening and identification of hybrid okra seeds. Hyperspectral imaging ; Linear discriminant analysis ; Principal component analysis ; Pattern recognition (psychology) ; Artificial intelligence ; Support vector machine ; Chemometrics ; Mathematics ; Discriminative model ; Calibration ; Partial least squares regression ; Computer science ; Statistics ; Machine learning Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Advanced Chemical Sensor Technologies
Authors: Thierry Balliau | Mélisande Blein‐Nicolas | Michel Zivy
Source: Proteomes (article, 2018-01-30)
Field: Chemistry — Spectroscopy

Evaluation of Optimized Tube-Gel Methods of Sample Preparation for Large-Scale Plant Proteomics The so-called tube-gel method is a sample preparation protocol allowing for management of SDS for protein solubilization through in-gel protein trapping. Because of its simplicity, we assumed that once miniaturized, this method could become a standard for large scale experiments. We evaluated the performances of two variants of the miniaturized version of the tube-gel method based on different solubilization buffers (Tris-SDS or urea-SDS). To this end, we compared them to two other digestion methods: (i) liquid digestion after protein solubilization in the absence of SDS (liquid method) and (ii) filter-aided sample preparation (FASP). As large-scale experiments may require long term gel storage, we also examined to which extent gel aging affected the results of the proteomics analysis. We showed that both tube-gel and FASP methods extracted membrane proteins better than the liquid method, while the latter allowed the identification and quantification of a greater number of proteins. All methods were equivalent regarding quantitative stability. However, important differences were observed regarding post-translational modifications. In particular, methionine oxidation was higher with the tube-gel method than with the other methods. Based on these results, and considering time, simplicity, and cost aspects, we conclude that the miniaturized tube-gel method is suitable for sample preparation in the context of large-scale experiments. Chromatography ; Sample preparation ; Context (archaeology) ; Chemistry ; Solubilization ; Sample (material) ; Materials science ; Biochemistry ; Biology Advanced Proteomics Techniques and Applications ; Biotin and Related Studies ; Muscle metabolism and nutrition
Authors: Tiina Rissanen | Petteri Parkkila | Artturi Koivuniemi | Jussi Lahti | Tapani Viitala | Mari Kallioinen | Mika Mänttäri | Alex Bunker
Source: Separation and Purification Technology (article, 2018-05-23)
Field: Chemistry — Electrochemistry

Characterization of membrane–foulant interactions with novel combination of Raman spectroscopy, surface plasmon resonance and molecular dynamics simulation Vanillin ; Membrane ; Chemistry ; Hydrogen bond ; Fouling ; Surface plasmon resonance ; Raman spectroscopy ; Molecule ; Adsorption ; Molecular dynamics ; Chemical engineering ; Membrane fouling ; Hydrophobic effect ; Protonation ; Organic chemistry ; Computational chemistry ; Nanoparticle Electrochemical Analysis and Applications ; Membrane Separation Technologies ; Spectroscopy and Quantum Chemical Studies
Authors: Chiara Cavaliere | Anna Laura Capriotti | Giorgia La Barbera | Carmela Maria Montone | Susy Piovesana | Aldo Laganà
Source: Molecules (review, 2018-11-27)
Field: Chemistry — Spectroscopy

Liquid Chromatographic Strategies for Separation of Bioactive Compounds in Food Matrices Nowadays, there is an increasing attention for nutraceuticals and, in general, bioactive compounds naturally present in food. Indeed, the possibility of preserving human health and preventing disease (e.g., cardiovascular diseases, cancer etc.) by the intake of healthy food is attractive for both consumers and food industries. In turn, research in this field was also prompted significantly, with the aim of characterizing these bioactive compounds and ascribe to them a specific activity. The bioactive compounds can belong to several chemical classes. However, their chemical diversity and presence in complex matrices, such as food, make it challenging both their isolation and characterization. To tackle this issue, efficient separation systems are needed, which are mainly based on chromatography. In this context, this mini-review aims to provide the reader with an overview of the most relevant and recent approaches for the separation of the most common bioactive compounds in food, in particular polyphenols, phenols, carotenoids, and peptides, by liquid chromatography approaches. Nutraceutical ; Context (archaeology) ; Complex matrix ; Polyphenol ; Chemistry ; Chromatographic separation ; Functional food ; Biochemical engineering ; Human health ; Biotechnology ; Chromatography ; Food science ; High-performance liquid chromatography ; Biology ; Organic chemistry ; Medicine ; Engineering ; Antioxidant Analytical Chemistry and Chromatography ; Chromatography in Natural Products ; Biochemical Analysis and Sensing Techniques
Authors: Shouzheng Su | Qi Liu | Jingyuan Liu | Hongsen Zhang | Rumin Li | Xiaoyan Jing | Jun Wang
Source: Scientific Reports (article, 2018-01-09)
Field: Chemistry — Inorganic Chemistry

Functionalized Sugarcane Bagasse for U(VI) Adsorption from Acid and Alkaline Conditions The highly efficient removal of uranium from mine tailings effluent, radioactive wastewater and enrichment from seawater is of great significance for the development of nuclear industry. In this work, we prepared an efficient U(VI) adsorbent by EDTA modified sugarcane bagasse (MESB) with a simple process. The prepared adsorbent preserves high adsorptive capacity for UO<sub>2</sub><sup>2+</sup> (pH 3.0) and uranyl complexes, such as UO<sub>2</sub>(OH)<sup>+</sup>, (UO<sub>2</sub>)<sub>2</sub>(OH)<sub>2</sub><sup>2+</sup> and (UO<sub>2</sub>)<sub>3</sub>(OH)<sub>5</sub><sup>+</sup> (pH 4.0 and pH 5.0) and good repeatability in acidic environment. The maximum adsorption capacity for U(VI) at pH 3.0, 4.0 and 5.0 is 578.0, 925.9 and 1394.1 mg/g and the adsorption capacity loss is only 7% after five cycles. With the pH from 3.0 to 5.0, the inhibitive effects of Na<sup>+</sup> and K<sup>+</sup> decreased but increased of Mg<sup>2+</sup> and Ca<sup>2+</sup>. MESB also exhibits good adsorption for [UO<sub>2</sub>(CO<sub>3</sub>)<sub>3</sub>]<sup>4-</sup> at pH 8.3 from 10 mg/L to 3.3 μg/L. Moreover, MESB could effectively extract U(VI) from simulated seawater in the presence of other metals ions. This work provided a general and efficient uranyl enriched material for nuclear industry. Uranyl ; Adsorption ; Bagasse ; Chemistry ; Uranium ; Effluent ; Nuclear chemistry ; Wastewater ; Seawater ; Alkali metal ; Ion ; Pulp and paper industry ; Waste management ; Organic chemistry ; Materials science ; Metallurgy Radioactive element chemistry and processing ; Geochemistry and Elemental Analysis ; Hydrocarbon exploration and reservoir analysis
Authors: Tao Yang | Jian Liu | Harry O. Finklea | Shiwoo Lee | William K. Epting | Rubayyat Mahbub | Tim Hsu | A. Salvador | Harry Abernathy | Gregory Hackett
Source: International Journal of Hydrogen Energy (article, 2018-07-17)
Field: Materials Science — Materials Chemistry

An efficient approach for prediction of Warburg-type resistance under working currents Multiphysics ; Solid oxide fuel cell ; Equivalent circuit ; Computer science ; Polarization (electrochemistry) ; Anode ; Electrical impedance ; Performance prediction ; Finite element method ; Biological system ; Mechanics ; Simulation ; Electrode ; Chemistry ; Voltage ; Physics ; Electrical engineering ; Engineering ; Thermodynamics Advancements in Solid Oxide Fuel Cells ; Fuel Cells and Related Materials ; Electrocatalysts for Energy Conversion
Authors: Nagaretnam Prahadeesh | M. Sithambaresan | Umaramani Mathiventhan
Source: Emerging Science Journal (article, 2018-12-13)
Field: Chemistry — Organic Chemistry

A Study on Hydrogen Peroxide Scavenging Activity and Ferric Reducing Ability of Simple Coumarins Coumarin compounds are Î´-lactones where α-pyrone ring is fused with benzene ring. Coumarins are widely distributed in the plant kingdom as well as they are very important in synthetic organic chemistry. Coumarins have great interest because of their abundance in nature and diverse pharmacological activities including antibacterial, antiviral, antipyretic, and anticoagulant, antioxidant, anti-inflammatory and anticancer. This study focused on synthesizing different simple Coumarins and studying their antioxidant activity. Four simple Coumarins (Coumarin (C1), 4-hydroxy coumarin (C2), 7-hydroxy coumarin (C3) and 7-hydoxy-4-methyl coumarin (C4)) were synthesized by using standard methods and were characterized by using UV, IR, 1H and 13C NMR spectra. Antioxidant activity of the simple Coumarins was studied by using standard FRAP assay and Hydrogen peroxide assay and expressed as FRAP value (mmol Fe2+/g) and IC50 value (mg/dm-3) respectively. Ascorbic acid was used as standard. All synthesized simple Coumarins showed both antioxidant activities. Hydroxyl Coumarins (C2, C3 and C4) showed higher activities in both cases than C1. Among the hydroxyl Coumarins C3 showed highest hydrogen peroxide scavenging activity and Ferric reducing capacity too. Antioxidant power of the tested simple Coumarins in decreasing order was C3, C2, C4 and C1 in both cases. But the hydrogen peroxide scavenging activity and Ferric reducing capacity of the all synthesized simple Coumarins were lower when compared to standard ascorbic acid. Chemistry ; Ascorbic acid ; Coumarin ; Hydrogen peroxide ; Antioxidant ; Ferric ; Peroxide ; Organic chemistry ; Food science Free Radicals and Antioxidants ; Synthesis of Organic Compounds ; Phytochemicals and Antioxidant Activities
Authors: Hongnan Cao | Mu Gao | Hongyi Zhou | Jeffrey Skolnick
Source: Communications Biology (article, 2018-12-06)
Field: Materials Science — Materials Chemistry

The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release Abstract Dihydrofolate reductase (DHFR) catalyzes the stereospecific reduction of 7,8-dihydrofolate (FH2) to (6s)-5,6,7,8-tetrahydrofolate (FH4) via hydride transfer from NADPH. The consensus Escherichia coli DHFR mechanism involves conformational changes between closed and occluded states occurring during the rate-limiting product release step. Although the Protein Data Bank (PDB) contains over 250 DHFR structures, the FH4 complex structure responsible for rate-limiting product release is unknown. We report to our knowledge the first crystal structure of an E. coli . DHFR:FH4 complex at 1.03 Å resolution showing distinct stabilizing interactions absent in FH2 or related (6R)-5,10-dideaza-FH4 complexes. We discover the time course of decay of the co-purified endogenous FH4 during crystal growth, with conversion from FH4 to FH2 occurring in 2–3 days. We also determine another occluded complex structure of E. coli DHFR with a slow-onset nanomolar inhibitor that contrasts with the methotrexate complex, suggesting a plausible strategy for designing DHFR antibiotics by targeting FH4 product conformations. Dihydrofolate reductase ; Product (mathematics) ; Chemistry ; Crystallography ; Reductase ; Stereochemistry ; Biochemistry ; Enzyme ; Mathematics ; Geometry Enzyme Structure and Function ; Folate and B Vitamins Research ; Porphyrin Metabolism and Disorders