jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Walaa Raheem | Alaa Kareem Niamah | Hussein O.M. Al-Dahmoshi | Ibrahim A. Murdas
Source: Egyptian Journal of Chemistry (article, 2021-08-18)
Field: Chemistry — Analytical Chemistry

Pesticide Residue Measurements in Raw Milk Based on Optical Spectrum and Neural Networks Pesticide residue has become as one of the major food adulterants as a result , rapid, simple, spectrophotometric method for pesticide residue measurement (bifenthrin, glyphosate) in milk sample based on UV-Vis spectrophotometer and Artificial neural network had been developed .The developed system detecting the milk contaminants like pesticide residue and classified it based on absorption spectrum. The hybrid system consists of UV-Vis spectrophotometer and neural package. The detection and classification processes depend on the readout of the UV-Vis spectroscopy to achieve the detection and recognition of all the samples by using Levenberg-Marquardt back propagation (LM-BP) neural network algorithm. The reported classification rate accuracy reached above 99.98%. Raw milk ; Residue (chemistry) ; Pesticide residue ; Artificial neural network ; Pesticide ; Environmental science ; Raw material ; Biological system ; Chemistry ; Food science ; Agronomy ; Computer science ; Artificial intelligence ; Biology ; Organic chemistry Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Water Quality Monitoring and Analysis
Authors: Showkat Ahmad Mir | Binata Nayak
Source: Research Square (preprint, 2021-11-23)
Field: Chemistry — Organic Chemistry

Molecular Dynamic Simulations and Binding Free Energy Evaluations of Thiazolo-[2,3-b] Quinazolinone Derivatives With wtEGFR-TKD and "TMLR" Mutant EGFR-TKD Abstract Cancer causes innumerable deaths every year globally. Breast cancer and non-small cell lung carcinoma (NSCLC) are the most prevalent worldwide. The epidermal growth factor receptor tyrosine kinases play a pivotal role in manifestations of cellular signals in carcinoma cells and thus are endorsed as therapeutic targets in cancer management. EGFR-TKD is a good option for the treatment of cancer, but the resistance shown by first-generation TKIs leads to hyperphosphorylation, overexpression, and mutations of EGFR-TKD. The new molecular scaffolds of thiazolo-[2,3-b] quinazolinones were evaluated against EGFR-TKD via molecular docking simulations and thereby linked with molecular dynamic simulations to identify the ligand stability with EGFR-TKD’s. The binding energy of thiazolo-[2,3-b] quinazolinones is approximately similar to that of reference molecules found against both wild type wtEGFR-TKD and EGFR-TKD mutant "TMLR" (T790M/L858R) in this study. According to ADMET analysis, thiazolo-[2,3-b] quinazolinone derivatives (5ab, 5aq, and 5bq) are safe. The stability was investigated at an atomistic level by molecular dynamic simulations, and the strength of the bindings was calculated by the molecular mechanics Poisson-Boltzmann surface areas continuum solvation MM-PBSA method. The RMSD, radius of gyration, and SASA trajectories were studied in detail. The ΔGbind generated by heterocyclic 5aq thiazolo-[2,3-b] quinazolinone was found to be -63.723 ± 0.419 kJ/mol against the EGFR-TKD mutant "TMLR" and it was -51.551 ± 0.409 kJ/mol against wtEGFR-TKD. This study concludes that the top ranked complexes 5ab, 5aq, and 5bq with both wild and mutated types of EGFR-TKD corroborate that thiazolo-[2,3-b] quinazolinone derivatives, like the FDA-approved drug erlotinib, may be potent inhibitors of EGFR-TKD for patients with NSCLC. Epidermal growth factor receptor ; Chemistry ; T790M ; Molecular dynamics ; Mutant ; Molecular mechanics ; Cancer research ; Computational chemistry ; Receptor ; Biology ; Biochemistry ; Gefitinib Quinazolinone synthesis and applications ; Synthesis and Characterization of Heterocyclic Compounds ; Cancer therapeutics and mechanisms
Authors: Weliton Pedro Batiston | Emanuel Carrilho
Source: Brazilian Journal of Analytical Chemistry (article, 2021-06-01)
Field: Chemistry — Spectroscopy

The Importance and Challenges for Analytical Chemistry in Proteomics Analysis Although Linus Pauling had an exceptional scientific contribution to the study of chemical bonds, reported in his book The Nature of Chemical Bond, the lousy image he got for the X-ray diffraction drove him to an unstable structure with an unreal DNA triple helix publication. Oppositely, for the consecration of James Watson &amp; Francis Crick, they had the opportunity to enter science history using the right image of X-ray to propose the famous DNA double helix structure correctly. This chapter of science is an excellent example of how analytical chemistry performance affects horizons and scientific advances. Today the complexity of the systems is more significant and understanding how all proteins truly work into cells and organisms is the current challenge from proteomics. Comprehending how analysis is carried out and how instruments work could promote new insights to improve the analytical performance in proteomics. Here we described an overview based on our expertise on the analytical chemistry toolkit for proteomics analysis: shotgun, bottom-up, middle-down, top-down, and native proteomics, and their inherent instrumentation technologies. In addition, a detailed discussion of the analytical figures of merit in proteomics analysis is provided. We also address the limitations in multidimensional liquid chromatography and tandem mass spectrometry platforms. Furthermore, we present some perspectives in bioinformatics, mathematical modeling simulations, and chemometrics tools, as well. Proteomics ; Data science ; Computer science ; Chemistry ; Nanotechnology ; Materials science Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Microbial Metabolic Engineering and Bioproduction
Authors: Manuel Matzinger | Adrian Vasiu | Mathias Madalinski | Fränze Müller | Florian Stanek | Karl Mechtler
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-10-22)
Field: Chemistry — Spectroscopy

Mimicked synthetic ribosomal protein complex for benchmarking crosslinking mass spectrometry workflows ABSTRACT The field of cross-linking mass spectrometry has matured to a frequently used tool for the investigation of protein structures as well as interactome studies up to a system wide level. The growing community generated a broad spectrum of applications, linker types, acquisition strategies and specialized data analysis tools, which makes it challenging, especially for newcomers, to decide for an appropriate analysis workflow. Therefore, we here present a large and flexible synthetic peptide library as reliable instrument to benchmark crosslinkers with different reactive sites as well as acquisition techniques and data analysis algorithms. Additionally, we provide a tool, IMP-X-FDR, that calculates the real, experimentally validated, FDR, compares results across search engine platforms and analyses crosslink properties in an automated manner. The library was used with the reagents DSSO, DSBU, CDI, ADH, DHSO and azide-a-DSBSO and data were analysed using the algorithms MeroX, MS Annika, XlinkX, pLink 2, MaxLynx and xiSearch. We thereby show that the correct algorithm and search setting choice is highly important to improve ID rate and FDR in combination with software and sample-complexity specific score cut-offs. When analysing DSSO data with MS Annika, we reach high identification rates of up to ∼70 % of the theoretical maximum (i.e. 700 unique lysine-lysine cross-links) while maintaining a low real FDR of &lt; 3 % at cross-link level and with high reproducibility, representatively showing that our test system delivers valuable and statistically solid results. Graphical abstract Workflow ; Computer science ; Benchmark (surveying) ; Data mining ; Benchmarking ; Identification (biology) ; False discovery rate ; Software ; Chemistry ; Database ; Biology ; Programming language Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; RNA and protein synthesis mechanisms
Authors: Sema Çelik
Source: Gümüşhane Üniversitesi Fen Bilimleri Enstitüsü Dergisi (article, 2021-01-25)
Field: Chemistry — Analytical Chemistry

Kitosan-şeker pancarı posası biyokompozit sorban sisteminin anyonik boyarmadde biyosorpsiyon potansiyeli Bu çalışmada endüstriyel bir atık olan şeker pancarı posası kitosan ile immobilize edilmiş ve elde edilen biyokompozit materyal sulu çözeltilerden Asit Kırmızısı 1 ve Reaktif Kırmızısı 2 boyarmaddelerinin giderimi için kullanılmıştır. Biyokompozit sorbanın renk giderim performansı, başlangıç çözelti pH’sı, sorban miktarı, başlangıç boyarmadde derişimi, denge süresi ve iyonik şiddetin bir fonksiyonu olarak incelenmiştir. Optimum biyosorpsiyon koşullarında (pH: 3.0, biyokompozit sorban miktarı: 0.01 g, denge süresi:10 dk) biyokompozitin boyarmadde giderim verimleri AK1 için %81.23, RK2 için ise %86.79 olarak kaydedilmiştir. Biyokompozit sistemin renk giderim dinamikleri kinetik ve izoterm modellemeleriyle incelenmiştir. Biyosorpsiyon prosesi en iyi yalancı birinci derece kinetik modeli ve Langmuir izoterm modeli ile tanımlanmıştır. Biyokompozitin maksimum tek tabakalı biyosorpsiyon kapasitesi Asit Kırmızısı 1 için 358.027 mg g-1, Reaktif Kırmızısı 2 için ise 379.228 mg g-1, olarak hesaplanmıştır. Boyarmadde-biyokompozit sorban olası etkileşimleri zeta potansiyeli, IR ve SEM analizleriyle karakterize edilmiştir. Sonuçlar, geliştirilen biyokompozit sorbanın oldukça yüksek renk giderim kapasitesi ile sulu ortamdan anyonik boyarmadde uzaklaştırılması için etkili bir alternatif olabileceğini göstermiştir. Chemistry Dye analysis and toxicity ; Adsorption and biosorption for pollutant removal ; Dyeing and Modifying Textile Fibers
Authors: Serene Joy | Ashmitha Kishan Shetty | Rajamanickam Deveswaran | Jayaraman Anbu | Manasa Biligowda Latha | Shivani Selvappa | Siddique Sha Muhammed Hussain | Hussain | D Basu | R Kulkarni | O Garraud | J.-D Tissot | B Oudelaar | J Peerbooms | R Huis In't Veld | A Vochteloo | D Samarkanova | S Cox | D Hernandez | L Rodriguez | R Casaroli-Marano | A Madrigal | S Querol | G Giannaccare | A Carnevali | C Senni | L Logozzo | V Scorcia | G Yassin | M Dawoud | R Wasfi | A Maher | A Fayez | S Yildirim | S Fu | K Kim | H Zhou | C Lee | A Li | S Kim | S Wang | J Mao | F Damiri | Y Bachra | C Bounacir | A Laaraibi | M Berrada | B Moorthy | L Iyer | E Topp | J Cameron | H Butler | D Anderson | L Christie | L Confield | K Spalding | D Finlayson | S Murray | Z Panni | C Rinaldi | A Sala | A Theakstone | M Baker | R Silva | T Pereira | A Souza | P Ribeiro | L Da Silva | S Montalvo | L De | A Justo-Junior | S Da | J Cunha Jnior | S Huber | C Oliveira | J Annichino-Bizzacchi | X Lei | Y Yang | G Shan | Y Pan | B Cheng | P Cheng | X Xue | J Su | M Lu | J Meng | P Oneto | J Etulain | N Orlando | C Pellegrino | C Valentini | M Bianchi | O Barbagallo | S Sparnacci | F Forni | T Fontana | L Teofili | J Bujok | M Gsior-Gogowska
Source: Letters in Applied NanoBioScience (article, 2021-09-12)
Field: Materials Science — Biomaterials

A Nuclear Magnetic Resonance and Fourier-Transform Infrared Spectroscopic Study of Lyophilized Umbilical Cord Blood Platelet Rich Plasma Cord blood platelet-rich plasma is regarded as a potential therapeutic agent with wound healing and regenerative purposes. It has many advantages, such as availability, universal use, and being rich in regenerative tissue factors. To characterize the Umbilical Cord Blood Platelet Rich Plasma (UCB-PRP), umbilical cord blood is collected from healthy mothers in sterile vacutainers. Platelet-rich plasma was extracted after two sets of centrifugations and lyophilized using the freeze-drying method. The samples are subjected to physicochemical characterization using Nuclear Magnetic Resonance (NMR) and Fourier-Transform Infrared (FTIR) Spectroscopy. This translational approach provided evidence of clinical effectiveness for understanding physiology and pathophysiology at the molecular level. Accordingly, FTIR and NMR studies provided information on the structural stability of protein molecules present in UCB-PRP. Umbilical cord ; Fourier transform infrared spectroscopy ; Platelet-rich plasma ; Platelet ; Chemistry ; Cord blood ; Blood plasma ; Fourier transform ; Nuclear magnetic resonance ; Biomedical engineering ; Biochemistry ; Medicine ; Immunology ; Chemical engineering Electrospun Nanofibers in Biomedical Applications ; Tissue Engineering and Regenerative Medicine ; Periodontal Regeneration and Treatments
Authors: Adam Osinski | Miles H. Black | Krzysztof Pawłowski | Zhe Chen | Yang Li | Vincent S. Tagliabracci
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2021-04-13)
Field: Materials Science — Materials Chemistry

Structural and mechanistic basis for protein glutamylation by the kinase fold Summary The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ubiquitin ligases. The structural and mechanistic basis in which the kinase domain catalyzes protein glutamylation is unknown. Here we present cryo-EM reconstructions of SidJ:CaM:SidE reaction intermediate complexes. We show that the kinase-like active site of SidJ adenylates an active site Glu in SidE resulting in the formation of a stable reaction intermediate complex. An insertion in the catalytic loop of the kinase domain positions the donor Glu near the acyl-adenylate for peptide bond formation. Our structural analysis led us to discover that the SidJ paralog SdjA is a glutamylase that differentially regulates the SidE-ligases during Legionella infection. Our results uncover the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations and reveal an unappreciated level of SidE-family regulation. Adenylate kinase ; Effector ; Kinase ; Protein kinase domain ; Active site ; Ubiquitin ; Chemistry ; Biochemistry ; Protein kinase A ; Biology ; Enzyme Enzyme Structure and Function ; Neonatal Health and Biochemistry ; Legionella and Acanthamoeba research
Authors: Maryam Kouhkan | Fatemeh Ghanbary | Fatemeh Karimi
Source: Avicenna Journal of Clinical Microbiology and Infection (article, 2021-09-29)
Field: Chemistry — Organic Chemistry

Antibacterial Activity of New Compounds Based on Nanocomposites Background: Antimicrobial resistance is a major problem in treatment and public health, and it has been increasing over the last few decades. Hence, serious measurements are needed to overcome this challenge. In this study, we evaluated antibacterial and antifungal activity of some nanocomposites including titanium dioxide (5a), polyimide nanocomposites containing cerium oxide (5b), silver-titanium dioxide nanoparticles prepared under desired conditions (5c), polyaniline/wheat husk ash PANI /WHA (5d), Ag-TiO2 prepared by sol–gel route (5e), and cellulose-graphene (5f) against some bacterial and fungal strains, which are the most common agents in many infectious diseases. Methods: The nanoparticles were prepared in desired condition. The agar dilution and well agar diffusion methods were used for determination of inhibition zoon and minimum inhibitory concentration (MIC) during preliminary evaluation of antimicrobial activity against Staphylococcus aureus, Streptococcus pyogenes, Pseudomonas aeruginosa, Escherichia coli and Candida albicans. Results: The results showed that the nanocomposites had good activity against gram-negative bacteria. Conclusions: Our results showed that the inhibitory activity of these nanocomposites on gram-negative bacteria was better than gram-positive bacteria. Antimicrobial ; Minimum inhibitory concentration ; Antibacterial activity ; Nanocomposite ; Candida albicans ; Agar diffusion test ; Bacteria ; Staphylococcus aureus ; Agar dilution ; Pseudomonas aeruginosa ; Titanium dioxide ; Agar ; Silver nanoparticle ; Microbiology ; Chemistry ; Nanoparticle ; Materials science ; Biology ; Nanotechnology Synthesis of Tetrazole Derivatives ; Dendrimers and Hyperbranched Polymers ; Advanced Nanomaterials in Catalysis
Authors: Yong-Hyuk Kwon | Sol Choi | Hye-Seul Yoon | Hee-Seon Bang
Source: Journal of Welding and Joining (article, 2021-04-02)
Field: Materials Science — Metals and Alloys

Weldability of Aluminum Alloy and Hot Dip Galvanized Steel by AC Pulse MIG Brazing This study investigates the weldability of dissimilar materials, such as Al6061-T6 aluminum alloy and hot dip galvanized (GI) steel, via AC pulse metal inert gas (MIG) brazing. Notably, the brazing mechanism was investigated for different electrode negative (EN) ratios. The results showed that as the amount of deposition increased with the EN ratio, throat thickness, wetting length, and leg length also tended to increase. Furthermore, it was confirmed that as the EN ratio increased, a thin intermetallic compound (IMC) layer was deposited due to the suppression of IMC growth caused by the low heat input at the joint interface. Brazing ; Materials science ; Intermetallic ; Weldability ; Metallurgy ; Galvanization ; Alloy ; Welding ; Aluminium ; Gas metal arc welding ; Layer (electronics) ; Composite material ; Arc welding Hydrogen embrittlement and corrosion behaviors in metals ; Welding Techniques and Residual Stresses ; Corrosion Behavior and Inhibition
Authors: Elizabeth J. Kautz | Wufei Ma | Arun Baskaran | Aritra Chowdhury | Vineet V. Joshi | Bülent Yener | D. Lewis
Source: Microscopy and Microanalysis (article, 2021-07-30)
Field: Materials Science — Materials Chemistry

Image-driven discriminative and generative methods for establishing microstructure-processing relationships relevant to nuclear fuel processing pipelines An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the 'Save PDF' action button. Discriminative model ; Generative grammar ; Computer science ; Pipeline transport ; Action (physics) ; Artificial intelligence ; Engineering ; Mechanical engineering ; Physics Machine Learning in Materials Science ; Mineral Processing and Grinding ; Nuclear Physics and Applications
Authors: Galen T. Craven
Source:  (preprint, 2021-11-10)
Field: Materials Science — Materials Chemistry

Analytical solutions of the Arrhenius-Semenov problem for constant volume burn Analytical solutions to the Semenov thermal ignition problem for constant volume burn governed by Arrhenius reaction kinetics are derived. Specifically, an approximate analytical solution technique for the Arrhenius-Semenov differential equation is derived for reaction orders $n \in \mathbb{R}_{>0}$ and exact solutions are also constructed for reaction orders $n \in \mathbb{N}: n \leq 3$. The approximation technique relies on expansion of the respective nondominant terms in the differential equation at the lower and upper bounds of the reaction progress variable in order to create a pair of integrable series. The two integrated series are then connected to create a single continuous analytical solution. Excellent agreement is observed between the analytical approximation and solutions obtained numerically. The presented approximation constitutes a simple and robust strategy for solving the Arrhenius-Semenov problem analytically. Ode ; Arrhenius equation ; Constant (computer programming) ; Volume (thermodynamics) ; Order of reaction ; Thermodynamics ; First order ; Applied mathematics ; Order (exchange) ; Exponential function ; Mathematics ; Exponential decay ; Reaction rate constant ; Variable (mathematics) ; Reaction rate ; Chemistry ; Activation energy ; Kinetics ; Mathematical analysis ; Physics ; Computer science ; Physical chemistry ; Classical mechanics ; Nuclear physics ; Economics Graphene research and applications
Authors: Kumaran Baskaran | Colin W. Wilburn | Jonathan R. Wedell | Leonardus M. I. Koharudin | Eldon L. Ulrich | Adam D. Schuyler | Hamid R. Eghbalnia | Angela M. Gronenborn | Jeffrey C. Hoch
Source:  (preprint, 2021-07-01)
Field: Chemistry — Spectroscopy

Anomalous Amide Proton Chemical Shifts as Signatures of Hydrogen Bonding to Aromatic Sidechains Abstract. Hydrogen bonding between an amide group and the p-π cloud of an aromatic ring was first identified in a protein in the 1980s. Subsequent surveys of high-resolution X-ray crystal structures found multiple instances, but their preponderance was determined to be infrequent. Hydrogen atoms participating in a hydrogen bond to the p-π cloud of an aromatic ring are expected to experience an upfield chemical shift arising from a shielding ring current shift. We survey the Biological Magnetic Resonance Data Bank for amide hydrogens exhibiting unusual shifts as well as corroborating nuclear Overhauser effects between the amide protons and ring protons. We find evidence that Trp residues are more likely to be involved in p-π hydrogen bonds than other aromatic amino acids, whereas His residues are more likely to be involved in hydrogen bonds with a ring nitrogen acting as the hydrogen acceptor. The p-π hydrogen bonds may be more abundant than previously believed. The inclusion in NMR structure refinement protocols of shift effects in amide protons from aromatic side chains, or explicit hydrogen bond restraints between amides and aromatic rings, could improve the local accuracy of side-chain orientations in solution NMR protein structures, but their impact on global accuracy is likely be limited. Hydrogen bond ; Amide ; Chemistry ; Ring (chemistry) ; Chemical shift ; Aromaticity ; Hydrogen ; Crystallography ; Low-barrier hydrogen bond ; Side chain ; Proton NMR ; Stereochemistry ; Molecule ; Organic chemistry ; Physical chemistry ; Polymer Molecular spectroscopy and chirality ; Protein Structure and Dynamics ; Advanced NMR Techniques and Applications
Authors: Yaoshu Xie | Kiyou Shibata | Teruyasu Mizoguchi
Source: Research Square (preprint, 2021-11-16)
Field: Materials Science — Materials Chemistry

Integrated structural reconstruction of unit structures of the meta-stable grain boundaries in diamond-structured materials presents first-order like phase transition. Abstract One of the important issues of studying grain boundaries (GBs) which has recently attracted increasing interests is to investigate the phase behavior of GBs that one GB with determined disorientation and plane orientation (known as macroscopic parameters) can exist as distinct phases and perform phase transition. While such an issue has been investigated in fcc and bcc metals, GB phases in other elemental materials have not been reported. This work by applying molecular dynamics (MD) simulation explored totally around 7000 meta-stable GB phases of the &lt;110&gt;∑9(22‾1‾) symmetric tilt GB of silicon, germanium and diamond carbon as diamond-structured elemental materials. Meta-stable phases commonly exist in different elements were discovered and some of them were successfully verified to be reasonable by first-principle simulation. The verified meta-stable GBs were subsequently proved to have different capability to transform to the ground-stable GB at elevated temperature under MD simulation and to perform different pre-melting behaviors. We discovered a bi-directional structural reconstruction mechanism of the unit structure belonging to one of the verified meta-stable phases, by which the unit structures can transform to identical unit structures of the ground-stable GB which can present ‘opposite orientation’. Through computing the kinetic barriers by nudged-elastic-band and annealing simulation using MD, the integral behavior of the unit structures’ reconstruction is found to be a first-order like phase transition. Our work extended the research on GB phases from metals to diamond-structured materials and discovered a new GB phase transition mechanism which has not been reported before. Diamond ; Materials science ; Diamond cubic ; Molecular dynamics ; Phase transition ; Phase (matter) ; Crystallography ; Chemical physics ; Condensed matter physics ; Chemistry ; Computational chemistry ; Physics ; Composite material Microstructure and mechanical properties ; Semiconductor materials and interfaces ; Ion-surface interactions and analysis