jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Stephen J. Valentine | Sandra Majuta | Anthony DeBastiani | Sara Macios | Kushani Attanayake | Peng Li
Source: ChemRxiv (preprint, 2022-03-31)
Field: Chemistry — Spectroscopy

Dual Capillary-based Vibrating Sharp-edge Spray Ionization (cVSSI) with On-line Solution-phase Hydrogen/Deuterium Exchange for Distinguishing Carbohydrates Isomers In-droplet hydrogen-deuterium exchange (HDX) combined with mass spectrometry (MS) has been used to characterize the reactivities of monosaccharide (3 pairs), disaccharide (4 pairs), and glycan (1 pair) isomer compounds. To accomplish in-droplet HDX, capillary vibrating sharp-edge spray ionization (cVSSI) employing a dual emitter tip setup is utilized. The solution-phase HDX technique is shown to be extremely reproducible for these measurements such that several different isomer sets can be distinguished by their unique isotopic distributions in the mass spectrum. The results are discussed in light of their applicability toward identifying metabolite compounds in complex metabolomics mixtures. Chemistry ; Deuterium ; Mass spectrometry ; Ionization ; Hydrogen–deuterium exchange ; Hydrogen ; Glycan ; Monosaccharide ; Analytical Chemistry (journal) ; Capillary action ; Chromatography ; Atomic physics ; Materials science ; Organic chemistry ; Ion ; Physics Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Advanced Chemical Sensor Technologies
Authors: Rakesh Kumar Sharma
Source: Cancer therapy & Oncology International Journal (article, 2022-11-09)
Field: Chemistry — Spectroscopy

New Approaches of proteomics in cancer and stem cells: Part I: from Basic Research to Clinical Application Proteomic analysis based on the separation and identification of proteins/peptides is a powerful tool for discovering new biomarkers.Twodimensional differential gel electrophoresis (2D-DIGE), the ProteinChip array®, ClinProt®, and liquid chromatography are known as separation technologies.Although the detection and identification of proteins/peptides could be performed using mass spectrometry (MS), the types of MS used are diverse and the characteristics depend on the ionization method (e.g., matrix-assisted laser desorption/ionization [MALDI], surfaceenhanced laser desorption/ionization [SELDI], and electrospray ionization [ESI]) and mass analyzer (e.g., time-of-flight [TOF], quadrupole [Q], and ion trap [IT]).The diverse proteomic systems that couple separation technologies with MS have been successfully applied to search for cancer biomarkers in biological fluid such as serum.Until now, many cancer biomarkers have been reported to be identified from serum and plasma.In order to identify diagnostic biomarkers of hepatocellular carcinoma (HCC) and adult T-cell leukemia (ATL), which are both human viral malignancies, we have been analyzing sera from patients using the ProteinChip array®-SELDI system and MALDI-TOF-TOF-MS.In this review, we present an overview of proteomic technologies used to search for biomarkers and cancer biomarkers discovered by these technologies, including our data on HCC and ATL.Cancer diagnosis using these proteomic biomarkers is also described. Proteomics ; Computational biology ; Data science ; Computer science ; Biology ; Genetics Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; Cancer Research and Treatments
Authors: Mei-Qing Zuo | Rui-Xiang Sun | Meng‐Qiu Dong
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-07-01)
Field: Chemistry — Spectroscopy

D/E-rich peptides are less suitable than D/E-deficient peptides for identification by negative-ion HCD due to scarce production of sequencing ions from multiply charged precursors ABSTRACT Highly acidic, D/E-rich peptides or proteins are difficult to identify by positive-ion-mode mass spectrometry (MS), and negative-ion-mode MS is an attractive but insufficiently explored alternative. Based on high-resolution and accurate-mass MS analysis of 115 synthetic peptides of 5-28 amino acids, we confirmed that higher-energy collisional dissociation (HCD) of deprotonated peptides induced abundant backbone or side-chain neutral losses (NL), and updated the ranking list of NLs by abundance. The most abundant fragment ion types are y- &gt; x-, z- &gt; c- if the NL ions are included, or c- &gt; y- &gt; z- &gt; b- if not. The most frequent side-chain NLs involve amino acids C, S, T, D, E, N, Q, and R. Although NL of CO 2 is common for all peptides, it is markedly enhanced in D/E-containing peptides. Long peptides and D/E-rich peptides are prone to carrying multiple negative charges. HCD spectra produced from multiply deprotonated peptides have a lower fraction of sequencing ions (i.e., a-, b-, c-, x-, y-, z- ions) than those produced from 1 - ([M-H] - ) and 2 - ([M-2H] 2- ) precursors. Based on the above findings, we predict that under negative-ion HCD, D/E-rich peptides should be difficult to identify and that choosing a protease to generate peptides containing fewer D/E residues will improve identification of highly acidic proteins. Chemistry ; Deprotonation ; Ion ; Peptide ; Amino acid ; Mass spectrometry ; Dissociation (chemistry) ; Stereochemistry ; Biochemistry ; Chromatography ; Organic chemistry Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Analytical Chemistry and Chromatography
Authors: Nemanja Vuksanovic | Dante A. Serrano | Brandon M. Patterson | N.R. Silvaggi
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-04-02)
Field: Materials Science — Materials Chemistry

Engineering a more specific <i>E. coli</i> glyoxylate/hydroxypyruvate reductase for coupled steady state kinetics assays ABSTRACT The E. coli glyoxylate reductase/hydroxypyruvate reductase A (EcGhrA) was investigated as a coupling enzyme to monitor the transamination of 2-ketoarginine and glycine by the L-enduracididine biosynthetic enzyme MppQ. Surprisingly, 2-ketoarginine proved to be an efficient substrate for EcGhrA. Since the promiscuity of EcGhrA prevented its use as a coupling enzyme to monitor the aminotransferase activity of MppQ, we set about engineering a more specific variant. X-ray crystal structures of EcGhrA were determined in the unliganded state, as well as with glyoxylate and 2-ketoarginine bound. The electron density maps of EcGhrA with 2-ketoarginine bound showed weak electron density for the side chain of this substrate, complicating the choice of active site residues to target for site-directed mutagenesis. The structure of the complex did, however, suggest that the side chain of W45 could interact with the guanidinium group of 2-ketoarginine. We therefore generated the EcGhrA W45F variant and tested it for activity with 2-ketoarginine, glyoxylate, oxaloacetate, α-ketoglutarate, α-oxofuranacetic acid, phenyl pyruvate, 3-mercaptopyruvate and 2-ketobutyric acid. The W45F variant exhibited a ∼10-fold decrease in the specificity constant (k cat /K M ) for 2-ketoarginine, while the reaction with glyoxylate was not significantly impaired. The reactions of the W45F variant with the alternative substrates oxaloacetate and α-ketoglutarate were also impaired. Thus, the W45F variant is a less promiscuous enzyme than the wild-type. This engineered EcGhrA W45F variant could be generally useful as a coupling system for enzymes that produce glyoxylate, such as 4-hydroxy-2-oxoglutarate aldolase or isocitrate lyase. Glyoxylate cycle ; Transamination ; Chemistry ; Enzyme ; Stereochemistry ; Citrate synthase ; Active site ; Biochemistry ; Reductase ; Amino acid ; Substrate (aquarium) ; Biology Enzyme Structure and Function ; Amino Acid Enzymes and Metabolism ; Biochemical and Molecular Research
Authors: Vera Silva | Sofia Benfeito | Eva Gil-Martins | Inês Costa | Fernando Remião | Fernanda Borges | Renata Silva
Source: RevSALUS - Revista Científica da Rede Académica das Ciências da Saúde da Lusofonia (article, 2022-04-06)
Field: Chemistry — Organic Chemistry

In vitro neuroprotective effects of dua-acting antiparkinsonians e r Introduction: Parkinson Disease (PD) is the second most common neurodegenerative disorder [1], being characterized by the degeneration of dopaminergic neurons of substantia nigra pars compacta [2]. PD is also associated with iron accumulation within the brain, which triggers a specific form of regulated cell death called ferroptosis, further leading to dopamine (DA) depletion [3]. Currently, no effective treatment exists for stopping or delaying PD progression. Instead, the available drugs are predominantly directed to symptoms relief, keeping the course of the disease unchanged [4]. Objectives: Thus, the main goal of this study was to evaluate the potential in vitro neuroprotective effects of newly synthetized smart dual-acting molecules (3-hydroxypyridin-4-ones). These compounds were developed in the scope of the FCT-funded project "COMT4brain" and demonstrated the ability of simultaneously chelate iron and inhibit COMT, allowing to restore DA levels. Neuroprotection ; In vitro ; Medicine ; Pharmacology ; Biology ; Biochemistry Carbohydrate Chemistry and Synthesis ; Synthesis of Organic Compounds ; Bioactive Compounds and Antitumor Agents
Authors: A Novikov | N North | J Lloyd | J Renshaw | M Xu | L Newsome | K Morris
Source:  (article, 2022-07-06)
Field: Chemistry — Inorganic Chemistry

Diversity and possible metabolic activity of the microbial community in nitrate- and radionuclide-contaminated groundwater Radionuclide ; Nitrate ; Groundwater ; Contamination ; Environmental chemistry ; Environmental science ; Diversity (politics) ; Chemistry ; Ecology ; Biology ; Geology ; Physics ; Sociology Radioactive element chemistry and processing
Authors: Chad ten Pas | Ke Du | Long Pan | Ruo‐Qian Wang | Shiyou Xu
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-06-17)
Field: Materials Science — Surfaces, Coatings and Films

Understanding the Dynamics of Fluid-Structure Interaction with an Air Deflected Microfluidic Chip (ADMC) Abstract A deformable microfluidic system and a fluidic dynamic model have been successfully coupled to understand the dynamic fluid-structure interaction in transient flow, designed to understand the dentine hypersensitivity caused by hydrodynamic theory. The Polydimethylsiloxane thin sidewalls of the microfluidic chip are deformed with air pressure ranging from 50 to 500 mbar to move the liquid meniscus in the central liquid channel. The displacement is recorded and compared with our new theoretical model derived from the unsteady Bernoulli equation. We show that our theoretical model can well predict the ending point of the liquid displacement as well as the dynamics process, regardless of the wall thickness. Moreover, an overshooting and oscillation phenomenon is observed by reducing the friction factor by a few orders which could be the key to explain the dentine hypersensitivity caused by the liquid movement in the dentine tubules. Polydimethylsiloxane ; Fluidics ; Microfluidics ; Bernoulli's principle ; Mechanics ; Materials science ; Meniscus ; Oscillation (cell signaling) ; Displacement (psychology) ; Dynamics (music) ; Fluid dynamics ; Flow (mathematics) ; Transient (computer programming) ; Nanotechnology ; Chemistry ; Optics ; Physics ; Engineering ; Acoustics ; Thermodynamics ; Electrical engineering ; Computer science Surface Modification and Superhydrophobicity ; Advanced Sensor and Energy Harvesting Materials ; Heat Transfer and Boiling Studies
Authors: Laurent Peltier
Source: SPIRE - Sciences Po Institutional REpository (preprint, 2022-04-12)
Field: Materials Science — Materials Chemistry

Development and thermomechanical study of a High Temperature and High Entropy Shape Memory Alloy Conventional metal alloys are made up of a majority element, such as copper, iron, or nickel, associated with other elements present in smaller quantities. In 2004, Cantor et al. produced an alloy composed of 5 elements with an equiatomic distribution. These high entropy alloys (HEAs) are of growing interest for applications in extreme environments thanks to their good behavior at high temperatures and their high chemical stability. On the other hand, high-temperature shape memory alloys (HT-SMAs) are subject to a short lifetime due to phase precipitation at grain boundaries above 200°C. In this thesis, alloys combining the high temperature strength of HEAs and the high temperature shape memory effect (HT SMAs) have been developed in cold crucible and have been thoroughly investigated in terms of microstructure, metallurgical state and thermomechanical responses. The study of these new materials with high entropy and containing high melting point metals has obliged us to adapt our means of heat treatment and related analysis. The activation temperatures of these alloys as well as the phases present have been identified by coupling temperature bending tests. The lifetime of these new HE&HT-SMAs has been tested in stress bending and temperature fatigue tests. The behavior of the new AHEs is also compared to the behavior of the usual AMFs, in particular the binary alloys NiTi and TiNb. The microstructural evolutions at the origin of the high entropy optimization have been studied by X-ray diffraction, optical and electronic microscopy, DSC and mechanical tests. This work concludes with a study of the Ms temperature estimation for HE-SMAs as a function of the chemical composition of the alloy. The proposed equation is based on the study of the compositions of HE-SMAs from the scientific literature and the alloys produced for this thesis work. Alloy ; Materials science ; Shape-memory alloy ; High entropy alloys ; Thermomechanical processing ; Metallurgy ; Thermodynamics ; Mechanical engineering ; Composite material ; Engineering ; Physics Shape Memory Alloy Transformations
Authors: M. Đaković | M. Pisačić | O. Mišura
Source: Acta Crystallographica Section A Foundations and Advances (article, 2022-08-23)
Field: Materials Science — Biomaterials

Mechanically responsive crystals: tuning flexibilty through fine-tuning intermolecular interactions Responsiveness of crystalline solids, in particular molecular crystals, to a variety of external stimuli has become a highly desired property as it enables their application in emerging technologies.Although adaptability of crystals to external stimuli other than sole mechanical force has been widely reported, mechanically stimulated flexibility is still relatively rarely observed among molecular crystals and the rationale behind those responses is far from being fully understood [1].Coordination polymers, in addition to being ideal model systems for exploring structural prerequisites for delivery of a specific mechanical response [2], have recently offered a range of not hitherto observed mechanical behaviours of crystalline materials [3][4][5].Supramolecular interactions, in particular hydrogen and halogen bonds, emerged as one of the key structural features in the delivery of a targeted mechanical response, and their role in fine-tuning those responses, as well as a correlation of their influence in crystal packing and mechanical response, will be demonstrated on several recent examples [3][4][5][6][7]. Intermolecular force ; Materials science ; Chemical physics ; Fine-tuning ; Nanotechnology ; Crystallography ; Chemistry ; Physics ; Molecule ; Organic chemistry Calcium Carbonate Crystallization and Inhibition ; Supramolecular Self-Assembly in Materials
Authors: Takamasa Tsukamoto | Tetsuya Kambe | Kimihisa Yamamoto
Source: Chemistry Letters (article, 2022-06-13)
Field: Materials Science — Polymers and Plastics

Equable Fine-tuning Techniques of Bimetallic Co-complexation in Dendrimer for Cluster Synthesis Covering a Wide Range of Composition Precise preparation of multinuclear bimetallic dendrimer complexes with finely-controlled compositions was investigated for template synthesis of alloy clusters by using platinum and tin. An ordered complexation behavior of metal salts in the dendrimer with imine units enabled bimetallic co-accumulations in a dendrimer template while combinations of metal salts with various acidity achieved the formation of 27 patterns of complexes. This fine-tuning technique of compositions in the dendrimer complexes leads to precise synthesis of alloy clusters covering wider range of composition. Precise preparation of multinuclear bimetallic dendrimer complexes with finely-controlled compositions was investigated for template synthesis of alloy clusters using platinum and tin. An ordered complexation behavior of metal salts in the dendrimer with imine units enabled bimetallic co-accumulations in a dendrimer template while combinations of metal salts with various acidity achieved the formation of various patterns of complexes. Bimetallic strip ; Dendrimer ; Chemistry ; Imine ; Tin ; Alloy ; Metal ; Combinatorial chemistry ; Platinum ; Cluster (spacecraft) ; Inorganic chemistry ; Polymer chemistry ; Catalysis ; Organic chemistry Dendrimers and Hyperbranched Polymers ; Nanocluster Synthesis and Applications ; Gold and Silver Nanoparticles Synthesis and Applications
Authors: Hessan Khalid | Sung Gue Heo | Mi‐Hye Lee | Kyoung‐Tae Park | Soong Ju Oh | Seok‐Jun Seo
Source: SSRN Electronic Journal (article, 2022-01-01)
Field: Chemistry — Organic Chemistry

Versatile Synthesis of 1-D Β-Feooh Nanoparticles with Fine-Tuned Exchange Biasing and Weak Ferromagnetic Effect Biasing ; Ferromagnetism ; Nanoparticle ; Exchange bias ; Materials science ; Nanotechnology ; Condensed matter physics ; Voltage ; Physics ; Magnetization ; Magnetic anisotropy ; Quantum mechanics Nanomaterials for catalytic reactions
Authors: Sunggeun Shim | Woon Bae Park | Jungmin Han | Jinhyeok Lee | Byung Do Lee | Jin‐Woong Lee | Jung Yong Seo | S. J. Richard Prabakar | Su Cheol Han | Satendra Pal Singh | Chan‐Cuk Hwang | Docheon Ahn | Sang-Il Han | Kyusung Park | Kee‐Sun Sohn | Myoungho Pyo
Source: Advanced Science (article, 2022-10-01)
Field: Chemistry — Inorganic Chemistry

Optimal Composition of Li Argyrodite with Harmonious Conductivity and Chemical/Electrochemical Stability: Fine‐Tuned Via Tandem Particle Swarm Optimization (Adv. Sci. 28/2022) Tandem Particle Swarm Optimization In article number 2201648 by Kee‐Sun Sohn, Myoungho Pyo, and co‐workers, a two‐step optimization algorithm (tandem particle swarm optimization) is applied to rapidly identify the optimal argyrodite with the highest attainable σ (ion) in a multidimensional search space involving a huge number of compositions and processing conditions. Each particle (bee) is searching for the best candidate by exchanging information through the social behavior. The identified argyrodite exhibits enhanced σ (ion) and improved stability against moisture and high voltage and, as an all‐solid‐state battery, would deliver higher capacities, particularly during fast charge–discharge cycles. [Image: see text] Particle swarm optimization ; Tandem ; Materials science ; Battery (electricity) ; Particle (ecology) ; Stability (learning theory) ; Voltage ; Electrochemistry ; Chemical engineering ; Computer science ; Mathematical optimization ; Chemistry ; Electrical engineering ; Algorithm ; Physics ; Composite material ; Thermodynamics ; Mathematics ; Engineering ; Electrode ; Power (physics) ; Machine learning Radioactive element chemistry and processing ; Chemical Synthesis and Characterization ; Polyoxometalates: Synthesis and Applications
Authors: Zhen‐Nan Shen | Yuxuan Xu | Chenyu Wang | Bo Qiao
Source: ChemPhotoChem (article, 2022-03-21)
Field: Materials Science — Materials Chemistry

Cover Feature: Fine‐Tuning the Thermal Relaxation Dynamics of Indigo‐Based Photoswitches Using Selective Non‐Covalent Interactions Without Chemical Modification (ChemPhotoChem 4/2022) The Cover Feature shows a molecular complex formed between the Z-isomer of an indigo-based photoswitch and a lithium cation. The formation of this complex stabilizes the Z-isomer and slows the thermal relaxation rate of this photoswitch. In contrast, the uncomplexed molecules have a faster relaxation rate, as shown by the motion blur. Cover image designed by Julie Liu (SIAIS, ShanghaiTech University). More information can be found in the Research Article by Bo Qiao and co-workers. Photoswitch ; Relaxation (psychology) ; Cover (algebra) ; Covalent bond ; Chemistry ; Chemical physics ; Molecule ; Photochemistry ; Organic chemistry Photochromic and Fluorescence Chemistry ; Porphyrin and Phthalocyanine Chemistry ; Luminescence and Fluorescent Materials
Authors: Jun He | Xinhe Ye | Zhiqing Liu | Liangming Tang | Jieying Hu | Zhengtao Xu
Source: ChemRxiv (preprint, 2022-03-13)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Telltale Diamagnetism at 50 K of a Coordination Polymer System The synthesis of coordination polymers (e.g., Prussian blue) is as old as modern chemistry itself, but never stops surprising people. We here report superconductivity observed of a designer coordination polymer system sporting the chemically soft mercaptan and hard carboxyl groups. The mercapto-carboxyl (dubbed Mercarb, or QiuSuo in Mandarin Pinyin) synergy hints at Daoism and here carries over from the molecular to the solid state: the soft sulfur donors bond with Co2+/Ni2+ (or other transition metal ions) to afford 2D sheets for charge transport, while the interlayer metal-carboxylate domain is more ionic and mediates the transition into the superconductive state. Besides the flexible QiuSuo design, this CP system is suited for doping (e.g., with μ2-OH2 units to effect charge balance by transforming into μ2-OH-), in order to fine-tune the electron-hole balance, and to achieve high-temperature superconductivity. Diamagnetism ; Coordination polymer ; Ionic bonding ; Superconductivity ; Charge (physics) ; Polymer ; Crystallography ; Chemistry ; Prussian blue ; Electron configuration ; Materials science ; Ion ; Chemical physics ; Inorganic chemistry ; Condensed matter physics ; Crystal structure ; Physics ; Electrochemistry ; Physical chemistry ; Organic chemistry ; Magnetic field ; Quantum mechanics Organic and Molecular Conductors Research ; Magnetism in coordination complexes ; Metal-Organic Frameworks: Synthesis and Applications
Authors: MITCH JACOBY
Source: C&EN Global Enterprise (article, 2022-02-28)
Field: Materials Science — Materials Chemistry

Customizing alloy catalysts When it comes to catalytic activity, more isn’t always better. Overly active catalysts may be hard to control; finding the sweet spot can be tricky. That job may be easier now thanks to a study showing the effects of fine-tuning the composition of catalytic alloys ( Nat. Chem. 2022, DOI: 10.1038/s41557-021-00855-3 ). Manufacturers make tens of millions of metric tons of polyethylene annually. The ethylene starting material typically contains trace amounts of acetylene, which must be removed because it can poison polymerization catalysts. Polymer suppliers generally remove the impurity using palladium catalysts to convert acetylene to ethylene. But palladium’s high activity means t he catalyst can overhydrogenate acetylene, forming unwanted ethane and generating dangerous levels of heat. To help tackle the problem, Michael J. Janik, Robert M. Rioux, and coworkers at Pennsylvania State University studied a family of palladium-zinc alloys. They used solid-state synthesis methods to precisely tailor the alloys, Acetylene ; Catalysis ; Palladium ; Polyethylene ; Ethylene ; Materials science ; Polymer ; Zinc ; Chemical engineering ; Polymer chemistry ; Organic chemistry ; Chemistry ; Metallurgy ; Composite material ; Engineering Machine Learning in Materials Science ; Cloud Computing and Resource Management ; Catalysis and Hydrodesulfurization Studies