jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Luke Higgins | Henry Gerdes | Pedro R. Cutillas
Source: Biochemical Journal (article, 2023-03-24)
Field: Chemistry — Spectroscopy

Principles of phosphoproteomics and applications in cancer research Phosphorylation constitutes the most common and best-studied regulatory post-translational modification in biological systems and archetypal signalling pathways driven by protein and lipid kinases are disrupted in essentially all cancer types. Thus, the study of the phosphoproteome stands to provide unique biological information on signalling pathway activity and on kinase network circuitry that is not captured by genetic or transcriptomic technologies. Here, we discuss the methods and tools used in phosphoproteomics and highlight how this technique has been used, and can be used in the future, for cancer research. Challenges still exist in mass spectrometry phosphoproteomics and in the software required to provide biological information from these datasets. Nevertheless, improvements in mass spectrometers with enhanced scan rates, separation capabilities and sensitivity, in biochemical methods for sample preparation and in computational pipelines are enabling an increasingly deep analysis of the phosphoproteome, where previous bottlenecks in data acquisition, processing and interpretation are being relieved. These powerful hardware and algorithmic innovations are not only providing exciting new mechanistic insights into tumour biology, from where new drug targets may be derived, but are also leading to the discovery of phosphoproteins as mediators of drug sensitivity and resistance and as classifiers of disease subtypes. These studies are, therefore, uncovering phosphoproteins as a new generation of disruptive biomarkers to improve personalised anti-cancer therapies. Phosphoproteomics ; Computational biology ; Proteomics ; Drug discovery ; Computer science ; Systems biology ; Biology ; Cancer biomarkers ; Bioinformatics ; Kinase ; Cancer ; Protein phosphorylation ; Protein kinase A ; Biochemistry ; Genetics ; Gene Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Xiangtang Li | Hang Hu | Julia Laskin
Source: Analytica Chimica Acta (article, 2023-09-17)
Field: Chemistry — Spectroscopy

High-resolution integrated microfluidic probe for mass spectrometry imaging of biological tissues Mass spectrometry imaging ; Chemistry ; MALDI imaging ; Biomolecule ; Image resolution ; Mass spectrometry ; Microfluidics ; Resolution (logic) ; Biological imaging ; Desorption electrospray ionization ; High resolution ; Biological tissue ; Nanotechnology ; Ionization ; Desorption ; Matrix-assisted laser desorption/ionization ; Optics ; Materials science ; Chemical ionization ; Chromatography ; Ion ; Remote sensing ; Physics ; Computer science ; Artificial intelligence Mass Spectrometry Techniques and Applications ; Ion-surface interactions and analysis ; Microfluidic and Capillary Electrophoresis Applications
Authors: Mahmoud A. Tantawy | Israa A. Wahba | Samah S. Saad | Nesrin K. Ramadan
Source: BMC Chemistry (article, 2023-06-07)
Field: Chemistry — Analytical Chemistry

Classical versus chemometrics tools for spectrophotometric determination of fluocinolone acetonide, ciprofloxacin HCl and ciprofloxacin impurity-A in their ternary mixture Green, simple, accurate and robust univariate and chemometrics assisted UV spectrophotometric approaches have been adopted and validated for concurrent quantification of fluocinolone acetonide (FLU), ciprofloxacin HCl (CIP) together with ciprofloxacin impurity-A (CIP imp-A) in their ternary mixture. Double-divisor ratio spectra derivative (DDRD) method has been used for determination of FLU. On the other hand, the first (D<sup>1</sup>) and second (D<sup>2</sup>) derivative approaches have been applied for the quantification of CIP and CIP imp-A, respectively. For the ratio difference (RD), derivative ratio (DR), and mean centering of ratio spectra (MC) methods, CIP and its impurity A have been simultaneously determined. The acquired calibration plots were linear over the concentration range of 0.6-20.0 μg/mL, 1.0-40.0 μg/mL and 1.0-40.0 μg/mL for fluocinolone acetonide, ciprofloxacin HCl, and ciprofloxacin impurity-A, respectively. The chemometrics methods namely; partial least squares (PLS) and artificial neural networks (ANN) were used for the concurrent determination of the three adopted components via using twenty-five mixtures as calibration set and fifteen mixtures as validation one. The investigated approaches were validated in accordance with International Council for Harmonisation (ICH) guidelines, and statistically compared with the official ones. The proposed methods were acceptably applied to the examination of FLU and CIP in their pure powders and pharmaceutical ear drops. Chemometrics ; Fluocinolone acetonide ; Ternary operation ; Ciprofloxacin ; Chromatography ; Chemistry ; Medicine ; Computer science ; Dermatology ; Antibiotics Analytical Methods in Pharmaceuticals ; Antibiotics Pharmacokinetics and Efficacy ; Analytical Chemistry and Chromatography
Authors: Shahriar Mostufa | Parsa Yari | Bahareh Rezaei | K. Xu | Jiajia Sun | Zongqian Shi | Kai Wu
Source: Journal of Physics D Applied Physics (article, 2023-07-28)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Metamaterial as perfect absorber for high sensitivity refractive index based biosensing applications at infrared frequencies Abstract In this paper, we introduce a novel design of a metamaterial unit cell absorber, which is based on a metal/insulator/metal sandwich structure. The design is subjected to comprehensive finite element method computational analysis to ensure accurate and reliable results. The proposed metamaterial sandwich structure demonstrates exceptional absorption performance, achieving a nearly perfect absorption rate of 99.996% at the resonance infrared frequency of 39.8 THz. To provide a detailed theoretical explanation of nearly perfect absorption, we employ the effective medium theory, impedance matching, and field distribution analysis. Additionally, we have optimized the structural parameters of the sensor to maximize its absorption peak. This includes optimizing the thickness of the gold (Au) layer (from 0.03 to 0.28 μ m), the distance between the L shape corners (from 0.60 to 0.90 μ m), and the thickness of SiC dielectric spacer (from 0.20 to 0.45 μ m). Furthermore, we showcase the remarkable sensitivity of the proposed metamaterial unit cell in detecting subtle changes in the refractive index through the implementation of a sensing medium setup in our model. Remarkably, we achieve a frequency shift sensitivity of 3.74 THz/RIU, along with a quality factor of 10.33, for a wide range of refractive indices (1.0–2.0). Moreover, for cancer detection, we attain a sensitivity of 3.5 THz/RIU. These findings highlight the exceptional performance of our approach in accurately detecting changes in refractive index, making it a promising candidate for various sensing applications. The novelty of our work lies in the design of a metamaterial unit cell structure. This configuration exhibits several noteworthy features, including wide incident angle ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" overflow="scroll"> <mml:mi>θ</mml:mi> </mml:math> ) coverage up to 60°, polarization insensitivity, exceptional frequency shift sensitivity, high absorption peaks across a wide range of refractive indices, and the ability to distinguish cancer cells from healthy ones. Metamaterial ; Refractive index ; Materials science ; Sensitivity (control systems) ; Metamaterial absorber ; Impedance matching ; Absorption (acoustics) ; Terahertz radiation ; Dielectric ; Optoelectronics ; Optics ; Electrical impedance ; Tunable metamaterials ; Electronic engineering ; Physics Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Advanced Antenna and Metasurface Technologies
Authors: Sunil K. Joshi | Paul Piehowski | Tao Liu | Sara J.C. Gosline | Jason McDermott | Brian Druker | Elie Traer | Jeffrey Tyner | Anupriya Agarwal | Cristina E. Tognon | Karin Rodland
Source: The Annual Review of Pharmacology and Toxicology (review, 2023-09-22)
Field: Chemistry — Spectroscopy

Mass Spectrometry–Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools. Proteogenomics ; Computational biology ; Biology ; Proteomics ; Precision medicine ; Genomics ; Transcriptome ; Bioinformatics ; Gene ; Genetics ; Genome ; Gene expression Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Molecular Biology Techniques and Applications
Authors: Maylin Acosta | Ana Quiñones | Sandra Munera | José Miguel de Paz | J. Blasco
Source: Sensors (article, 2023-07-19)
Field: Chemistry — Analytical Chemistry

Rapid Prediction of Nutrient Concentration in Citrus Leaves Using Vis-NIR Spectroscopy The nutritional diagnosis of crops is carried out through costly foliar ionomic analysis in laboratories. However, spectroscopy is a sensing technique that could replace these destructive analyses for monitoring nutritional status. This work aimed to develop a calibration model to predict the foliar concentrations of macro and micronutrients in citrus plantations based on rapid non-destructive spectral measurements. To this end, 592 'Clementina de Nules' citrus leaves were collected during several months of growth. In these foliar samples, the spectral absorbance (430-1040 nm) was measured using a portable spectrometer, and the foliar ionomics was determined by emission spectrometry (ICP-OES) for macro and micronutrients, and the Kjeldahl method to quantify N. Models based on partial least squares regression (PLS-R) were calibrated to predict the content of macro and micronutrients in the leaves. The determination coefficients obtained in the model test were between 0.31 and 0.69, the highest values being found for P, K, and B (0.60, 0.63, and 0.69, respectively). Furthermore, the important P, K, and B wavelengths were evaluated using the weighted regression coefficients (BW) obtained from the PLS-R model. The results showed that the selected wavelengths were all in the visible region (430-750 nm) related to foliage pigments. The results indicate that this technique is promising for rapid and non-destructive foliar macro and micronutrient prediction. Partial least squares regression ; Micronutrient ; Absorbance ; Kjeldahl method ; Nutrient ; Chemistry ; Linear regression ; Spectroscopy ; Analytical Chemistry (journal) ; Environmental science ; Mathematics ; Nitrogen ; Environmental chemistry ; Chromatography ; Statistics ; Physics Spectroscopy and Chemometric Analyses ; Leaf Properties and Growth Measurement ; Water Quality Monitoring and Analysis
Authors: Franz Bamer | Firaz Ebrahem | Bernd Markert | Benjamin Stamm
Source: Archives of Computational Methods in Engineering (article, 2023-01-20)
Field: Materials Science — Materials Chemistry

Molecular Mechanics of Disordered Solids Abstract Disordered solids are ubiquitous in engineering and everyday use. Although research has made considerable progress in the last decades, our understanding of the mechanics of these materials is, at best, in an embryonic state. Since the nature of disorder complicates the realization of physically meaningful continuum-mechanical models, particle-based molecular descriptions provide a powerful alternative. This paper reviews the numerical realization of classical molecular dynamics from an engineer’s perspective, starting with selecting potential functions, boundary conditions, time integration, and thermodynamic ensembles. Then, we discuss the concept of the potential energy landscape and the computational realization of the most suitable minimization methods. Subsequently, we discuss the algorithms necessary to numerically generate disordered materials, considering their thermodynamic properties and structural identification. We comprehensively and critically review computational methods and strategies available to mimic disordered materials on a molecular level and discuss some intriguing phenomena that are, to date, mostly ignored when applying models based on continuum-mechanical frameworks. We present the crucial difference between the shear response of a crystalline and a disordered structure. In this context, we elaborate on why it is beneficial to use an overdamped, athermal description to disentangle the complex deformation mechanics of disordered solids and comprehensively discuss the theory of the mechanics of disordered materials, including the problems of prediction and reversibility. Furthermore, we examine the fracture process on the nanoscale and investigate the response behavior to more complex deformation protocols. Finally, we provide critical conclusions, including challenges and future perspectives for engineers. Realization (probability) ; Context (archaeology) ; Statistical physics ; Computer science ; Continuum mechanics ; Physics ; Classical mechanics ; Mathematics ; Geology Material Dynamics and Properties ; Composite Material Mechanics ; Theoretical and Computational Physics
Authors: Nichlas Vous Christensen | Michael Væggemose | Nikolaj Bøgh | Esben Søvsø Szocska Hansen | Jonas Lynge Olesen | Yaewon Kim | Daniel B. Vigneron | Jeremy W. Gordon | Sune Nørhøj Jespersen | Christoffer Laustsen
Source: Magnetic Resonance in Medicine (article, 2023-08-01)
Field: Chemistry — Spectroscopy

A user independent denoising method for x‐nuclei <scp>MRI</scp> and <scp>MRS</scp> The strength of tMPPCA lies in the few-input approach, which generalizes well to different data sources. This makes the use of tMPPCA denoising a robust and versatile tool in x-nuclei imaging improvements and the preferred denoising method. Noise reduction ; Noise (video) ; Pattern recognition (psychology) ; Artificial intelligence ; Principal component analysis ; Tensor (intrinsic definition) ; Singular value decomposition ; Computer science ; Mathematics ; Nuclear magnetic resonance ; Algorithm ; Physics ; Image (mathematics) Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Tensor decomposition and applications
Authors: Dongmei Wei | Jesús D. Melgarejo | Lucas Van Aelst | Thomas Vanassche | Peter Verhamme | Stefan Janssens | Karlheinz Peter | Zhen‐Yu Zhang
Source: European Journal of Preventive Cardiology (article, 2023-03-21)
Field: Chemistry — Spectroscopy

Prediction of coronary artery disease using urinary proteomics A novel urinary proteomic classifier related to collagen metabolism, lipids, and inflammation showed potential for the risk prediction of CAD. Urinary proteome provides an alternative approach to personalized prevention. Medicine ; Coronary artery disease ; Internal medicine ; Cohort ; Receiver operating characteristic ; Area under the curve ; Confidence interval ; CAD ; Framingham Risk Score ; Cohort study ; Disease Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Adipokines, Inflammation, and Metabolic Diseases
Authors: Yoshimi Haga | Yuriko Minegishi | Koji Ueda
Source: Cancer Science (review, 2023-01-20)
Field: Chemistry — Spectroscopy

Frontiers in mass spectrometry–based clinical proteomics for cancer diagnosis and treatment Numerous omics studies, primarily genomics analyses, have been conducted to fully understand the molecular biological characteristics of cancer. In recent years, the depth of proteomic analysis, which comprehensively analyzes proteins and molecules that function directly in vivo, has increased dramatically. Proteomics using mass spectrometry (MS) is a promising technology to directly examine proteoforms, including post-translational modifications and variants originating from genomic aberrations. Recent advances in MS-based proteomics have enabled direct, in depth, and quantitative analysis of the expression levels of various cancer-related proteins, as well as their cancer-specific proteoforms, and proteins that fluctuate with cancer initiation and progression in cell lines and tissue samples. Additionally, the integration of proteomic data with genomic, epigenomic, and transcriptomic data has formed the growing field of proteogenomics, which is already yielding new biological and diagnostic knowledge. Deep proteomic profiling provides clinically useful information in various aspects, including understanding the mechanisms of cancer development and progression and discovering targets for diagnosis and drug development. Furthermore, it is expected to make a significant contribution to the promotion of personalized medicine. In this review, recent advances and impacts in MS-based clinical proteomics are highlighted with a focus on oncology. Proteomics ; Proteogenomics ; Computational biology ; Genomics ; Epigenomics ; Biomarker discovery ; Proteome ; Bioinformatics ; Biology ; Omics ; Cancer ; Personalized medicine ; Genome ; Genetics ; Gene ; Gene expression ; DNA methylation Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Sara Oudi | Ali Reza Oveisi | Saba Daliran | Mostafa Khajeh | Amarajothi Dhakshinamoorthy | Hermenegildo Garcı́a
Source: Nanomaterials (article, 2023-01-30)
Field: Materials Science — Materials Chemistry

A Porphyrin-Based Covalent Organic Framework as Metal-Free Visible-LED-Light Photocatalyst for One-Pot Tandem Benzyl Alcohol Oxidation/Knoevenagel Condensation A porphyrin-based covalent organic framework (COF), namely Porph-UOZ-COF (UOZ stands for the University of Zabol), has been designed and prepared via the condensation reaction of 5,10,15,20-tetrakis-(3,4-dihydroxyphenyl)porphyrin (DHPP) with 1,4-benzenediboronic acid (DBBA), under the solvothermal condition. The solid was characterized by spectroscopic, microscopic, and powder X-ray diffraction techniques. The resultant multifunctional COF revealed an outstanding performance in catalyzing a one-pot tandem selective benzylic C-H photooxygenation/Knoevenagel condensation reaction in the absence of additives or metals under visible-LED-light irradiation. Notably, the catalytic activity of the COF was superior to individual organic counterparts and the COF was both stable and reusable for four consecutive runs. The present approach illustrates the potential of COFs as promising metal-free (photo) catalysts for the development of tandem reactions. Knoevenagel condensation ; Porphyrin ; Catalysis ; Tandem ; Covalent bond ; Photocatalysis ; Benzyl alcohol ; Photochemistry ; Covalent organic framework ; Chemistry ; Condensation reaction ; Visible spectrum ; Materials science ; Metal ; Organic chemistry Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Advanced Photocatalysis Techniques
Authors: Vincent Monnier | Fabrice Odobel | Stéphane Diring
Source: Journal of the American Chemical Society (article, 2023-08-24)
Field: Chemistry — Inorganic Chemistry

Exploring the Impact of Successive Redox Events in Thin Films of Metal–Organic Frameworks: An Absorptiometric Approach Metal-organic frameworks (MOFs) featuring redox activity are highly appealing for electrocatalytic or charge accumulation applications. An important aspect in this field is the ability to address as many redox centers as possible in the material by an efficient diffusion of charges. Herein, we investigate for the first time the charge diffusion processes occurring upon two sequential one-electron reductions in an MOF thin film. Two pyrazolate-zinc(II)-based MOFs including highly electro-deficient perylene diimide (PDI) ligands were grown on conducting substrates, affording thin films with double <i>n</i>-type electrochromic properties as characterized by spectroelectrochemical analysis. In depth electrochemical and chronoabsorptiometric investigations were carried out to probe the charge diffusion in the MOF layers and highlighted significant differences in terms of diffusion kinetics and material stability between the first and second successive reduction of the redox-active PDI linkers. Our results show that MOFs based on multiredox centers are more sensitive to encumbrance-related issues than their monoredox analogues in the context of electrochemical applications, an observation that further underlines the fundamental aspect of careful pore dimensions toward efficient and fast ion diffusion. Chemistry ; Redox ; Electrochromism ; Diimide ; Electrochemistry ; Diffusion ; Context (archaeology) ; Metal-organic framework ; Perylene ; Nanotechnology ; Thin film ; Chalcogen ; Electrode ; Chemical physics ; Inorganic chemistry ; Organic chemistry ; Physical chemistry ; Molecule ; Adsorption ; Materials science ; Thermodynamics Metal-Organic Frameworks: Synthesis and Applications ; Electrochemical Analysis and Applications ; Conducting polymers and applications