jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Michael Plach
Source: OPUS Repository (Kooperativer Bibliotheksverbund Berlin-Brandenburg) (article, 2020-01-01)
Field: Chemistry — Organic Chemistry

Serotonin 5-HT2A - Dopamine D2 Receptor Heterodimers: Characterization and Functional Evaluation associated to the -subunit of the heterotrimeric G protein.Upon binding of an agonist, changes in the conformation of helical and intracellular domains induce the replacement of GDP by GTP and activate the G protein.Dissociating G and G subunits in turn modulate effector proteins triggering cellular signaling pathways (right panel). The concept of GPCR oligomerizationIt was originally hypothesized that GPCRs are expressed individually in the plasma membrane and function as monomeric units. 24In the 1980s, studies using purified receptors provided data major projections of dopamine neurons: The mesocortical pathway (light blue) projects from the ventral tegmental area towards cortical regions, the mesolimbic pathway (magenta) from the same origin to the nucleus accumbens.Neurons of the nigrostriatal pathway (dark blue) start in the substantia nigra and innervate the striatum.The tuberoinfundibular pathway (green) originates in the hypothalamus and ends in the pituitary gland.ctl NTS1R-D2LR 0 2 4 6 8 10 PLA / cell / field Dopamine receptor D2 ; Serotonin ; Dopamine ; Chemistry ; Neuroscience ; Receptor ; Biology ; Biochemistry Cyclopropane Reaction Mechanisms
Authors: David M. Smalley | Shawn S.‐C. Li | Lee M. Graves | Stephanie A. Zukowski | Gilles Lajoie | James D.R. Knight | Jacob P. Turowec | David W. Litchfield | Gary L. Johnson
Source: UNC Libraries (article, 2020-11-05)
Field: Chemistry — Spectroscopy

An Unbiased Proteomic Screen Reveals Caspase Cleavage Is Positively and Negatively Regulated by Substrate Phosphorylation Post-translational modifications of proteins regulate diverse cellular functions, with mounting evidence suggesting that hierarchical cross-talk between distinct modifications may fine-tune cellular responses. For example, in apoptosis, caspases promote cell death via cleavage of key structural and enzymatic proteins that in some instances is inhibited by phosphorylation near the scissile bond. In this study, we systematically investigated how protein phosphorylation affects susceptibility to caspase cleavage using an N-terminomic strategy, namely, a modified terminal amino isotopic labeling of substrates (TAILS) workflow, to identify proteins for which caspase-catalyzed cleavage is modulated by phosphatase treatment. We validated the effects of phosphorylation on three of the identified proteins and found that Yap1 and Golgin-160 exhibit decreased cleavage when phosphorylated, whereas cleavage of MST3 was promoted by phosphorylation. Furthermore, using synthetic peptides we systematically examined the influence of phosphoserine throughout the entirety of caspase-3, -7, and -8 recognition motifs and observed a general inhibitory effect of phosphorylation even at residues considered outside the classical consensus motif. Overall, our work demonstrates a role for phosphorylation in controlling caspase-mediated cleavage and shows that N-terminomic strategies can be tailored to study cross-talk between phosphorylation and proteolysis. Phosphorylation ; Cleavage (geology) ; Cell biology ; Substrate (aquarium) ; Chemistry ; Biology ; Ecology Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Metabolomics and Mass Spectrometry Studies
Authors: Valeria Nori | Antonio Arcadi | Armando Carlone | Fabio Marinelli | Marco Chiarini
Source:  (preprint, 2020-01-14)
Field: Chemistry — Organic Chemistry

Palladium-Catalyzed Regio- and Stereoselective Synthesis of Aryl and 3-Indolyl Substituted-4-Methylene- isoquinolin-1(<i>2H</i>)-ones. Cascade cyclocarbopalladation of the readily available aryl/alkyl-substituted propargylic amides containing an aryl iodide moiety, followed by Suzuki-Miyaura coupling with arylboronic acids, allowed an efficient regio- and stereoselective synthesis of tetrasubstituted-4-methylene-isoquinolin-1(2H)-ones. Moreover cascade cyclocarbopalladation, followed by reaction with 2- alkynyltrifluoroacetanilides, accomplished a double cyclization, to afford challenging 4-methylene-isoquinolin-1(2H)-ones bearing a 3-indolyl substituent, through aminopalladation/reductive elimination Moiety ; Stereoselectivity ; Chemistry ; Aryl ; Methylene ; Iodide ; Substituent ; Palladium ; Catalysis ; Alkyl ; Combinatorial chemistry ; Medicinal chemistry ; Organic chemistry Catalytic C–H Functionalization Methods ; Catalytic Alkyne Reactions ; Catalytic Cross-Coupling Reactions
Authors: Xia‐Li Ding | Yuan‐Qi Zhai | Tian Han | Weipeng Chen | You‐Song Ding | Yan-Zhen Zheng
Source: ChemRxiv (preprint, 2020-07-24)
Field: Materials Science — Electronic, Optical and Magnetic Materials

D4h Local Symmetric dysprosium(III) Single-Molecule Magnet with Energy Barrier Exceeding 2000 K &lt;p&gt;&lt;a&gt;&lt;/a&gt;&lt;a&gt;&lt;/a&gt;&lt;a&gt;&lt;b&gt;Three six-coordinate Dy(III) single-molecule magnets (SMMs) [Dy(O&lt;sup&gt;t&lt;/sup&gt;Bu)&lt;sub&gt;2&lt;/sub&gt;(L)&lt;sub&gt;4&lt;/sub&gt;]&lt;sup&gt;+&lt;/sup&gt; with &lt;i&gt;D&lt;/i&gt;&lt;sub&gt;4h&lt;/sub&gt; local symmetry are obtained by optimising the equatorial ligands. Compound 1 where L = 4-phenylpyridine shows an energy barrier (&lt;i&gt;U&lt;/i&gt;&lt;sub&gt;eff&lt;/sub&gt;) of 2075(11) K, which is the third largest &lt;i&gt;U&lt;/i&gt;&lt;sub&gt;eff&lt;/sub&gt;, and the first &lt;i&gt;U&lt;/i&gt;&lt;sub&gt;eff&lt;/sub&gt; &gt; 2000 K for SMMs with axial-type symmetry so far.&lt;/b&gt;&lt;/a&gt;&lt;/p&gt; Chemistry ; Dysprosium ; Crystallography ; Physics Magnetism in coordination complexes ; Porphyrin and Phthalocyanine Chemistry ; Lanthanide and Transition Metal Complexes
Authors: Claire Seydoux
Source: SPIRE - Sciences Po Institutional REpository (preprint, 2020-11-30)
Field: Materials Science — Biomaterials

Regulation of photosynthesis by a potassium transporter in the diatom Phaeodactylum tricornutum La lumière du soleil est la source d’énergie primaire sur dont dépendent directement ou indirectement tous les organismes pour leurs besoins métaboliques. Malgré les nombreux avantages de l’utilisation d’une source d’énergie abondante et inépuisable, la lumière est néanmoins intrinsèquement variable et intermittente. Afin de survivre, les organismes photosynthétiques doivent constamment adapter leur machinerie moléculaire de capture de la lumière, en particulier par l’induction de mécanismes de quenching non-photochimiques (NPQ). Le contrôle de l’équilibre entre photosynthèse et photoprotection s’effectue chez les plantes supérieures et les algues vertes par une régulation fine des composantes électrique et osmotique de la force proton motrice à travers la membrane des thylacoïdes. L’homéostasie ionique joue donc un rôle majeur dans la régulation de la photosynthèse. La modulation de la composition de la force proton motrice par des échangeurs ioniques est un moyen pour les organismes photosynthétiques de réguler efficacement l’induction du NPQ, c.à.d. en minimisant les pertes d’énergie tout en préservant la synthèse d’ATP.Les diatomées ont un rôle écologique primordial dans les océans, notamment par leur contribution à la mitigation du réchauffement climatique par leur rôle dans la pompe biogéochimique du carbone ou par leur rôle de source de nourriture pour l’ensemble de la vie marine. Nous avons montré chez la diatomée modèle Phaeodactylum tricornutum que le pH des thylacoïdes régule directement l’induction et la relaxation du NPQ. Nous avons ainsi affiné le modèle de la dynamique du NPQ chez P. tricornutum, où le contrôle cinétique du cycle des xanthophylles par le pH joue un rôle prépondérant.Nous avons identifié l’antiport proton/potassium KEA3 et déterminé qu’il est un régulateur important de la force proton motrice chez les diatomées. Par l’étude de mutants CRISPR-Cas9, nous avons observé que ce transporteur module le pH du lumen et ainsi permet d’adapter la réponse NPQ selon les conditions environnementales. KEA3 convertit la composante ΔpH de la force proton motrice en ΔΨ, et de ce fait n’induit aucune perte d’énergie et maintient donc la synthèse d’ATP. Phaeodactylum tricornutum ; Diatom ; Photosynthesis ; Potassium ; Transporter ; Environmental science ; Botany ; Chemistry ; Biology ; Biochemistry ; Organic chemistry Diatoms and Algae Research ; Algal biology and biofuel production
Authors: Katrina May VanderVliet
Source: Digital WPI (article, 2020-05-13)
Field: Materials Science — Biomaterials

Improving Large Scale Culture of Anchorage Dependent Cells Chronic diseases are a prevalent and expensive health conditions in the US, with 133 million people suffering from a chronic disease. Tissue engineering, particularly mesenchymal stem cell(MSC) approaches, show great potential in meeting the need for treatments. There is a need for an improved scaffold to promote proliferation of adherent cells within bioreactors. This project aims to solve this gap in technology by constructing a 3-D scaffold of a novel material that would solve production issues of MSC's. A literature review found materials that were nontoxic, flexible, and allowed cellular adhesion. Experiments quantified cell seeding and proliferation on varying materials to select a material for final design. A multilayer scaffold of stainless steel mesh was selected for final design. Scale (ratio) ; Computer science ; Geography Silk-based biomaterials and applications ; Viral Infectious Diseases and Gene Expression in Insects
Authors: Jason Baker
Source: Digital Scholarship - UNLV (University of Nevada Reno) (article, 2020-05-08)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Instrumentation and Measurement of Thermoelectric and Structural Properties of Binary Chalcogenides and Half-Heusler Alloys at Extreme Conditions Using a Paris-Edinburgh Press Understanding the high-pressure behavior of transport properties has been a driving force in the study of materials under extreme conditions for well over a century being pioneered by P.W. Bridgman in the early 20th century. Research dedicated to the study of these properties leads to a variety of important applications: exploration of insulator to semi-conductor to metal, structural, and electronic phase transitions, correlation of pressure-induced structural phase transitions and the electronic properties along phase boundaries, identifying electronic topological transitions, testing the validity of theoretical models and providing input parameters for calculations at high-pressure and high-temperature conditions, exploration of sample synthesis and behavior of electronic structure at extreme conditions, understanding the effects of chemical pressure when compared to chemical substitution, among a slew of other applications. This work's main goal was the design and development of a specialized sample cell assembly for use with a Paris-Edinburgh press capable of performing high-pressure and high-temperature (HPHT) electrical resistance, Seebeck coefficient, thermal conductivity measurements alongside energy-dispersive X-ray diffraction and X-ray radiography imaging up to 6 GPa and 500¡C to fully characterize the electrical, thermal, and structural properties of materials simultaneously at extreme conditions. This system has been installed at Argonne National Laboratory at the Advanced Photon Source at the Sector 16 BM-B beamline of the High-Pressure Collaborative Access Team and is now available to general users as a measurement technique. The results for pure elemental bismuth and the classical thermoelectric material PbTe are presented to demonstrate the capabilities of the system. With this system, we have also measured the electrical, thermal, and structural properties of SnTe and Mn-doped SnTe thermoelectric materials and the half-Heusler compounds TiNiSn and TiCoSb. Instrumentation (computer programming) ; Thermoelectric effect ; Materials science ; Binary number ; Engineering physics ; Thermodynamics ; Physics ; Computer science ; Mathematics Heusler alloys: electronic and magnetic properties ; Advanced Thermoelectric Materials and Devices ; Chalcogenide Semiconductor Thin Films
Authors: Kamil Sikora
Source: Advances in Thermal Processes and Energy Transformation (article, 2020-01-01)
Field: Materials Science — General Materials Science

Analysis of Resistance of Clad Composite of Structural Steel and Tombac to Stress at Elevated Temperature Technological operations, where the temperature gradient significantly affects the thermal expansion of the material, require care in the choice of thermal stress with respect to the material used. A high temperature gradient can result in an increase in thermal stresses, which can result in plastic deformation of the material or even its failure. Clad materials are generally very sensitive to thermal stress. Especially if it is a composite material composed of layers with very different coefficients of thermal conductivity and thermal expansion, in our case structural steel and tombac. The aim of this study is to use the finite element method to simulate the maximum allowable thermal stress of a rolled clad composite composed of layers of tombac (CuZn90/10) and a core of structural steel S235JR + N, when there is no plastic deformation. Materials science ; Composite material ; Temperature gradient ; Composite number ; Thermal conductivity ; Finite element method ; Thermal expansion ; Stress (linguistics) ; Thermal ; Deformation (meteorology) ; Core (optical fiber) ; Structural engineering ; Thermodynamics Material Properties and Applications ; Mechanical and Thermal Properties Analysis ; Additive Manufacturing and 3D Printing Technologies
Authors: Prabha Chuphal | Ishwar Venugopal | Snigdha Thakur
Source: Bulletin of Materials Science (preprint, 2020-08-01)
Field: Materials Science — Materials Chemistry

Formation of self-propelling clusters starting from randomly dispersed Brownian particles Colloid ; Cluster (spacecraft) ; Brownian motion ; Chemical physics ; Brownian dynamics ; Active matter ; Isotropy ; Nanotechnology ; Chemistry ; Chemical engineering ; Materials science ; Physics ; Physical chemistry ; Optics ; Computer science ; Biology Pickering emulsions and particle stabilization ; Micro and Nano Robotics ; Diffusion and Search Dynamics
Authors: Davide Marcato
Source: The International Islamic University Malaysia Repository (The International Islamic University Malaysia) (article, 2020-11-01)
Field: Chemistry — Physical and Theoretical Chemistry

Allometric scaling in biological and ecological systems Several biological variables (such as lifespan, metabolic rate, biomass production rate) were observed to depend on body mass through a simple power law, a phenomenon known as allometric scaling. Despite the bewildering diversity of living organisms, these allometric relations are typically found to hold over a range of masses spanning roughly 20 orders of magnitude. The mot famous allometric scaling law is probably Kleiber’s law, which states that the metabolic rate scales as body mass to the power 3/4. In this work, after presenting some empirical evidence of allometric scaling, I discuss some consequences of Kleiber’s law both at a level of individual organisms and whole ecosystems, in particular for forest communities. Also, a recently proposed model of oxygen consumption for in-vitro cell cultures, which aims to derive an allometric scaling relation for such constructs, is presented and discussed. Allometry ; Scaling ; Ecology ; Metabolic rate ; Power law ; Biomass (ecology) ; Scaling law ; Statistical physics ; Range (aeronautics) ; Biology ; Mathematics ; Statistics ; Physics thermodynamics and calorimetric analyses ; Greenhouse Technology and Climate Control ; Physiological and biochemical adaptations
Authors: U. I. Baby
Source: Journal of Plantation Crops (article, 2020-12-11)
Field: Chemistry — Analytical Chemistry

Iron filings in tea and its impact on the quality attributes of made tea and tea liquor Presence of iron filings in made tea (MT) is a serious issue in the tea industry with the implementation of FSSAI regulations. In this scenario, the estimation of iron filings in tea is a critical operation. Unfortunately, the widely accepted method of analysis as per IS 3633 is having a lot of limitations to obtain a reproducible result. Attempts were made to quantify the possible factors affecting the accuracy of the result. Critical attempts were also made to investigate the impact of iron filings on the quality attributes of made tea as well as the tea liquor. Other aspects like adulteration of tea with iron filings and its possible health hazards are also discussed. Business ; Green tea ; Quality (philosophy) ; Food science ; Chemistry Heavy Metals in Plants
Authors: Jeremiah van Baren
Source: eScholarship (California Digital Library) (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Optical Spectroscopy of Excitonic States and Interlayer Phonons in Atomically Thin Transition Metal Dichalcogenides Atomically thin transition metal dichalcogenides (TMDs, e.g. MoS$_2$, MoSe$_2$, WSe$_2$, and NbSe$_2$) exhibit remarkable properties which are relevant for science and novel applications, such as robust excitonic effects and well-defined valley degree of freedom. These electronic and vibrational properties are highly dependent on the layer number, stacking configuration, and charge density in the sample system and may be probed and manipulated through applied electromagnetic fields. As the quality and complexity of TMD-based devices has improved, so too has our ability explore the novel physics of these systems. In this dissertation, we probe exceptionally high-quality TMD devices to explore the detailed excitonic physics in monolayer WSe$_2$ and the interlayer phonons in MoS$_2$ and NbSe$_2$.First, we study monolayer WSe$_2$ devices encapsulated in boron nitride. The WSe$_2$ optical spectra exhibit diverse excitonic features, including the bright states, both the intra- and inter-valley dark states, and a collection of phonon replicas. We systematically study these spectral features and identify novel excitonic physics. For the bright states, we observe the 1s – 4s Rydberg excitons and measure their binding energy and exciton radii. When subject to high magnetic field, the bright trions (or exciton polarons) further exhibit pronounced charge-density-dependent oscillations due to Landau quantization. For the dark states, we identify the dark trions and demonstrate their distinct valley Zeeman effect and enhanced lifetime compared to bright trions. We further observe the intervalley exciton and characterize the intra- and inter-valley relaxation pathways available to the dark states. Finally, we investigate the exciton-phonon interactions and observe a collection of phonon-mediated relaxation processes. We demonstrate that these phonon replicas enable valley-selective optical detection of the dark excitons (trions).Beyond the monolayer, we study the interlayer shear and breathing mode phonons in multilayer MoS$_2$ and NbSe$_2$. We compare the phonon spectra of 2H- and 3R-stacked MoS$_2$ crystals and observe strong dependence of the shear modes on the layer stacking order. We further simulate the Raman spectra with a concise analytical model that considers the layer-by-layer structure of 2D crystals. Our Raman results provide an effective method to characterize the layer number and stacking order in 2D materials. Exciton ; Trion ; Condensed matter physics ; Phonon ; Monolayer ; Physics ; Spectroscopy ; Materials science ; Nanotechnology ; Quantum mechanics 2D Materials and Applications
Authors: Niels Møller Israelsen | Ilya P. Radko | Nicole Raatz | Jan Meijer | Ulrik L Andersen | Alexander Huck
Source: Materials for Quantum Technology (preprint, 2020-07-28)
Field: Materials Science — Materials Chemistry

Nitrogen-vacancy defect emission spectra in the vicinity of an adjustable silver mirror Abstract Optical emitters of quantum radiation in the solid state are important building blocks for emerging technologies making use of the laws of quantum mechanics. The efficiency of photon extraction from the host material is low for many solid-state systems due to their relatively high index of refraction. In this article we experimentally study the emission spectrum of an ensemble of nitrogen-vacancy defects implanted around 8 nm below the planar diamond surface and in the vicinity of a planar silver mirror. Scanning the distance between diamond and the mirror, we observe an enhancement of the spectral emission power by up to a factor of 3. We construct a model based on classical dipoles and elucidate the observations as being caused by interference in the far field of the emitters. Diamond ; Vacancy defect ; Planar ; Dipole ; Photon ; Emission spectrum ; Refractive index ; Materials science ; Spectral line ; Optics ; Radiation ; Physics ; Atomic physics ; Optoelectronics ; Molecular physics ; Condensed matter physics ; Quantum mechanics Diamond and Carbon-based Materials Research ; Laser-Matter Interactions and Applications ; Advanced Fiber Laser Technologies
Authors: Zoe Putman
Source: Maryland Shared Open Access Repository (USMAI Consortium) (article, 2020-11-15)
Field: Materials Science — Materials Chemistry

EVALUATING MODIFIED POLYHEDRIN PROMOTERS FOR IMPROVED CO-EXPRESSION OF KRAS4b While the baculovirus expression vector system (BEVS) has proved its ability to produce high quality recombinant proteins utilizing a eukaryotic host, limited improvements have been made with regards to expressing multiple proteins. Current co-expression protocols utilize native baculovirus promoters which have limited versatility and varying expression levels. This thesis work aims to address these limitations, through the evaluation of modified AcMNPV polyhedrin promoters with the end goal of identifying novel promoters that display varying levels of expression and provide greater control over the ratio of recombinant proteins produced in the cell. Initial promoter screening measured fluorescence output of an eGFP reporter. Promoters of the most interest were then evaluated for test protein expression to determine their ability to produce more complex proteins. Mutations within the minimal promoter region which disrupt critical promoter elements were found to severely impair promoter activity. On the other hand, those which altered the upstream region beyond the transcription start site had little influence on reporter gene levels. Mutations to the polyhedrin promoter CAGT motif which unexpectedly introduced an alternative translation start site (CAtg), appeared to significantly impact downstream gene expression. When this mutation was in-frame with the reporter gene, eGFP expression levels were found to exceed that of the native promoter. Conversely, minimal eGFP expression was observed when this mutation was not in-frame, suggesting potential use of uORFs to regulate expression. Findings from this work will aid future improvements to the BEVS and will be particularly useful for those seeking to improve co-expression protocols. Promoter ; Expression (computer science) ; Polyhedrin ; Computational biology ; Biology ; Computer science ; Gene expression ; Genetics ; Gene ; Programming language ; Recombinant DNA Thermal and Kinetic Analysis ; Inorganic Chemistry and Materials ; Molten salt chemistry and electrochemical processes