jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Randy Mujica
Source: HAL (Le Centre pour la Communication Scientifique Directe) (preprint, 2020-09-15)
Field: Materials Science — Biomaterials

Layer-by-Layer assembly of nanocellulose composite films with bio-inspired helicoidal superstructures Les proprietes optiques et mecaniques remarquables des materiaux naturels sont souvent associees a la complexite de leurs structures hierarchiques. L’une des plus complexes est la structure helicoidale, constituee de plusieurs couches de fibres alignees dont l’orientation tourne entre les couches voisines. Cette microstructure, dite de Bouligand, est associee a la resistance aux chocs accrue de la carapace de certains crustaces ainsi qu’a la reflexion preferentielle de la lumiere polarisee circulaire de certains fruits et insectes. Dans ce travail, nous avons fabrique des films minces bio-inspires complexes composes de nanofibrilles de cellulose et de poly(vinylamine) en utilisant l'approche couche-par-couche (LbL) et la pulverisation a incidence rasante (GIS), une methode permettant de controler l'alignement dans le plan de nano-objets anisotropes comme les nanofibrilles de cellulose. Nous avons demontre la possibilite de controler de facon independante la direction de l'alignement de chaque couche de cellulose. Ainsi, nous avons pu preparer des films minces avec une orientation unidirectionnelle, croisee ou helicoidale des nanofibrilles de cellulose, ce qu’il n’est pas possible de faire avec d’autres procedes de fabrication. Les proprietes optiques de ces films ont ete caracterisees par dichroisme circulaire et ellipsometrie spectroscopique a matrice de Mueller. Nous avons observe que la reponse chirale des films helicoidaux est controlee par le sens de rotation, le pas de l’helice et le nombre de couches avant rotation. Les proprietes mecaniques de ces films ont ete etudiees par differentes methodes de nanoindentation. La methodologie de fatigue par nano-contact a montre une ductilite accrue des films unidirectionnels et helicoidaux, qui peut etre indirectement liee a une absorption accrue de l'energie de ce materiau lors des sollicitations en raison de sa structure interne. Humanities ; Physics ; Materials science ; Nanocellulose ; Art ; Cellulose ; Chemistry Advanced Cellulose Research Studies ; Advanced Materials and Mechanics ; Plant Surface Properties and Treatments
Authors: Nirupa Nagaratnam | S.L. Delker | Rebecca Jernigan | Thomas E. Edwards | Janey Snider | Darren Thifault | Dewight Williams | Brent L. Nannenga | Mary R. Stofega | Lidia Sambucetti | James J. Hsieh | Andrew Flint | Petra Fromme | José M. Martín-García
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-11-27)
Field: Materials Science — Materials Chemistry

New Structural Insights into the Function of the Catalytically Active Human Taspase1 Abstract Proteases can play essential roles in severe human pathology, ranging from degenerative and inflammatory illnesses to infectious diseases, with some, such as Taspase1, involved in growth and progression of tumors at primary and metastatic sites. Taspase1 is a N-terminal nucleophile (Ntn)-hydrolase overexpressed in primary human cancers, coordinating cancer cell proliferation, invasion, and metastasis. Loss of Taspase1 activity disrupts proliferation of human cancer cells in vitro and in mouse xenograft models of glioblastoma, thus this protein has the potential to become a novel anticancer drug target. It belongs to the family of Ntn-hydrolases, a unique family of proteins synthesized as enzymatically inactive proenzymes that become activated upon cleavage of the peptide bond on the N-terminal side of a threonine residue, which then becomes the catalytic site nucleophile. The activation process simultaneously changes the conformation of a long domain at the C-terminus of the alpha-subunit for which no full-length structural information exists and its function is poorly understood. Here we present a novel cloning strategy to generate a fully active, circularly permuted form of Taspase1 to determine the crystallographic structure of catalytically active human Taspase1 to 3.04Å. We discovered that this region forms a long helical domain and is indispensable for the catalytic activity of Taspase1. Together, our study highlights the importance of this element for the enzymatic activity of Ntn-hydrolases and suggests that this long domain could be a novel target for the design of inhibitors with the potential to be developed into anticancer therapeutics. Active site ; Enzyme ; Hydrolase ; Proteases ; Cell growth ; In vitro ; Biochemistry ; Chemistry ; Function (biology) ; Cancer cell ; Biology ; Cell biology ; Cancer research ; Cancer ; Genetics Enzyme Structure and Function ; Protein Structure and Dynamics ; RNA and protein synthesis mechanisms
Authors: Tommaso De Marchi | Paul Theodor Pyl | Martin Sjöström | Stina Klasson | Hanna Sartor | Johan Malmström | Lars Malmström | Emma Niméus
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2020-05-07)
Field: Chemistry — Spectroscopy

“A Proteogenomic workflow reveals distinct molecular phenotypes related to breast cancer appearance” Abstract Proteogenomics approaches have enabled the generation of extensive information levels when compared to single omics technology studies, although burdened by massive experimental efforts. Here, we developed four improvements of a data independent acquisition mass spectrometry proteogenomics workflow to reveal distinct molecular phenotypes related to breast cancer appearance. We confirm mutational processes detectable at the protein level and highlight quantitation and pathway complementarity between RNA and protein data. Our analyses also validated previously established enrichments of estrogen receptor-dependent molecular features relating to transcription factor expression, and provided evidence for molecular differences related to the presence of mammographic appearances in spiculated tumors. In addition, several transcript-protein pairs displayed radically different abundance correlations depending on the overall clinical and pathological properties of the tumor. These results demonstrate that there are differentially regulated protein networks in clinically relevant sample groups, and that these protein networks influence both cancer biology as well as the abundance of potential biomarkers and drug targets. Proteogenomics ; Computational biology ; Biology ; Phenotype ; Proteomics ; Breast cancer ; Bioinformatics ; Cancer ; Genetics ; Gene expression ; Transcriptome ; Gene Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Gene expression and cancer classification
Authors: Traci L. Parry | Wei Huang | Brian C. Jensen | Ju Youn Beak | Timothy J. Stuhlmiller | Xin Chen | Sean T. Hicks | Noah Sciaky | Monte S. Willis | Jon S. Zawistowski | Steven P. Angus | Gary L. Johnson
Source: UNC Libraries (article, 2020-04-18)
Field: Chemistry — Organic Chemistry

Kinome and Transcriptome Profiling Reveal Broad and Distinct Activities of Erlotinib, Sunitinib, and Sorafenib in the Mouse Heart and Suggest Cardiotoxicity From Combined Signal Transducer and Activator of Transcription and Epidermal Growth Factor Receptor Inhibition BACKGROUND: Most novel cancer therapeutics target kinases that are essential to tumor survival. Some of these kinase inhibitors are associated with cardiotoxicity, whereas others appear to be cardiosafe. The basis for this distinction is unclear, as are the molecular effects of kinase inhibitors in the heart. METHODS AND RESULTS: We administered clinically relevant doses of sorafenib, sunitinib (cardiotoxic multitargeted kinase inhibitors), or erlotinib (a cardiosafe epidermal growth factor receptor inhibitor) to mice daily for 2 weeks. We then compared the effects of these 3 kinase inhibitors on the cardiac transcriptome using RNAseq and the cardiac kinome using multiplexed inhibitor beads coupled with mass spectrometry. We found unexpectedly broad molecular effects of all 3 kinase inhibitors, suggesting that target kinase selectivity does not define either the molecular response or the potential for cardiotoxicity. Using in vivo drug administration and primary cardiomyocyte culture, we also show that the cardiosafety of erlotinib treatment may result from upregulation of the cardioprotective signal transducer and activator of transcription 3 pathway, as co-treatment with erlotinib and a signal transducer and activator of transcription inhibitor decreases cardiac contractile function and cardiomyocyte fatty acid oxidation. CONCLUSIONS: Collectively our findings indicate that preclinical kinome and transcriptome profiling may predict the cardiotoxicity of novel kinase inhibitors, and suggest caution for the proposed therapeutic strategy of combined signal transducer and activator of transcription/epidermal growth factor receptor inhibition for cancer treatment. Kinome ; Sunitinib ; Erlotinib ; Cardiotoxicity ; Sorafenib ; Transcriptome ; Biology ; STAT protein ; Cancer research ; Computational biology ; Cell biology ; Signal transduction ; Epidermal growth factor receptor ; STAT3 ; Genetics ; Gene expression ; Receptor ; Gene ; Cancer Synthesis and biological activity ; Lung Cancer Treatments and Mutations ; Chemotherapy-induced cardiotoxicity and mitigation
Authors: Stuart R. Jefferys | Morgan C. Giddings
Source: UNC Libraries (article, 2020-10-31)
Field: Chemistry — Spectroscopy

Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data Motivation: Post-translational modifications are vital to the function of proteins, but are hard to study, especially since several modified isoforms of a protein may be present simultaneously. Mass spectrometers are a great tool for investigating modified proteins, but the data they provide is often incomplete, ambiguous and difficult to interpret. Combining data from multiple experimental techniques—especially bottom-up and top-down mass spectrometry—provides complementary information. When integrated with background knowledge this allows a human expert to interpret what modifications are present and where on a protein they are located. However, the process is arduous and for high-throughput applications needs to be automated. Mass spectrometry ; Markov chain Monte Carlo ; Top-down and bottom-up design ; Simulated annealing ; Computer science ; Chemistry ; Chromatography ; Algorithm ; Bayesian probability ; Artificial intelligence Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Nageswara R. Madamanchi | Marschall S. Runge
Source: UNC Libraries (article, 2020-11-02)
Field: Chemistry — Organic Chemistry

Redox signaling in cardiovascular health and disease Spatiotemporal regulation of the activity of a vast array of intracellular proteins and signaling pathways by reactive oxygen species (ROS) governs normal cardiovascular function. However, data from experimental and animal studies strongly support that dysregulated redox signaling, resulting from hyper-activation of various cellular oxidases or mitochondrial dysfunction, is integral to the pathogenesis and progression of cardiovascular disease (CVD). In this review, we address how redox signaling modulates the protein function, the various sources of increased oxidative stress in CVD, and the labyrinth of redox-sensitive molecular mechanisms involved in the development of atherosclerosis, hypertension, cardiac hypertrophy and heart failure, and ischemia–reperfusion injury. Advances in redox biology and pharmacology for inhibiting ROS production in specific cell types and subcellular organelles combined with the development of nanotechnology-based new in vivo imaging systems and targeted drug delivery mechanisms may enable fine-tuning of redox signaling for the treatment and prevention of CVD. Disease ; Redox ; Medicine ; Internal medicine ; Chemistry Free Radicals and Antioxidants ; Redox biology and oxidative stress
Authors: Jorge Duitama | Daniel Mahecha
Source: Faculty of 1000 Research Ltd (article, 2020-01-01)
Field: Chemistry — Spectroscopy

Referee report. For: CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets [version 2; peer review: 2 approved, 1 not approved] Sequence (biology) ; Protocol (science) ; Identification (biology) ; Field (mathematics) ; Matching (statistics) Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Bioinformatics and Genomic Networks
Authors: Suresh Mathivanan
Source: Faculty of 1000 Research Ltd (article, 2020-01-01)
Field: Chemistry — Spectroscopy

Referee report. For: CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets [version 2; peer review: 2 approved] Sequence (biology) ; Protocol (science) ; Identification (biology) ; Field (mathematics) ; Matching (statistics) Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Bioinformatics and Genomic Networks
Authors: Stacy A. Love | David Salas‐de la Cruz | Karleena Rybacki | Xiao Hu
Source:  (preprint, 2020-04-28)
Field: Materials Science — Biomaterials

Facile treatment to fine-tune cellulose crystals in cellulose-silk biocomposites through the use of hydrogen peroxide The study of protein-polysaccharide interactions as part of a biocomposite material is an area of research that carries implications in various fields of interest, such as the medical, environmental, and materials science. These blended polymer systems are extremely versatile as shown from a variety of biocomposites used by nature. However, to facilitate the deployment of such Cellulose ; Hydrogen peroxide ; SILK ; Polymer science ; Materials science ; Chemical engineering ; Polymer chemistry ; Chemistry ; Organic chemistry ; Composite material ; Engineering Silk-based biomaterials and applications
Authors: Stacy A. Love | David Salas‐de la Cruz | Karleena Rybacki | Xiao Hu
Source:  (preprint, 2020-04-28)
Field: Materials Science — Biomaterials

Facile treatment to fine-tune cellulose crystals in cellulose-silk biocomposites through the use of hydrogen peroxide The study of protein-polysaccharide interactions as part of a biocomposite material is an area of research that carries implications in various fields of interest, such as the medical, environmental, and materials science. These blended polymer systems are extremely versatile as shown from a variety of biocomposites used by nature. However, to facilitate the deployment of such Cellulose ; Hydrogen peroxide ; SILK ; Polymer science ; Materials science ; Peroxide ; Composite material ; Polymer chemistry ; Chemistry ; Chemical engineering ; Organic chemistry ; Engineering Silk-based biomaterials and applications
Authors: Guo‐Hong Ning | Zixuan Chen | Qiang Gao | Wei Tang | Zhongxin Chen | Cuibo Liu | Bingbing Tian | Xing Li | Kian Ping Loh
Source:  (article, 2020-05-04)
Field: Materials Science — Materials Chemistry

Salicylideneanilines-Based Covalent Organic Frameworks as Chemoselective Molecular Sieves Porous materials such as covalent organic frameworks (COFs) are good candidates for molecular sieves due to the chemical diversity of their building blocks, which allows fine-tuning of their chemical and physical properties by design. Tailored synthesis of inherently functional building blocks can generate framework materials with chemoresponsivity, leading to controllable functionalities such as switchable sorption and separation. Herein, we demonstrate a chemoselective, salicylideneanilines-based COF (SA-COF), which undergoes solvent-triggered tautomeric switching. This is unique compared to solid-state salicylideneanilines’ counterpart, which typically requires high energy input such as photo or thermal activation to trigger the enol–keto tautomerisim and cis–trans isomerization. Accompanying the tautomerization, the ionic properties of the COF can be tuned reversibly, thus forming the basis of size-exclusion, selective ionic binding or chemoseparation in SA-COF demonstrated in this work. Tautomer ; Molecular sieve ; Covalent bond ; Isomerization ; Ionic bonding ; Sorption ; Materials science ; Covalent organic framework ; Molecular switch ; Solvent ; Porosity ; Molecule ; Porous medium ; Nanotechnology ; Chemical engineering ; Chemistry ; Chemical physics ; Catalysis ; Organic chemistry ; Adsorption ; Ion Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Chemical Synthesis and Reactions
Authors: Frank D. King | London Wc H Aj
Source:  (article, 2020-01-01)
Field: Materials Science — Materials Chemistry

Energetic Tuning in Spirocyclic Conjugated Polymers The key to enabling their use in optoelectronic devices is precision control of the energy levels in a conjugated polymer. Traditionally, the incorporation of spirocycles into conjugated polymers was used to improve their microstructure of the solid state. Here we present a highly novel method of energy tuning by the use of spirocyclic electronically active systems. By altering a heteroatom’s size and oxidation state in an orthogonal spirocycle, we demonstrate energetic fine tuning in both the absorption and emission of a conjugated polymer. In addition, the synthesis of the highly novel spirocyclic conjugated triplet-decker polymers is presented. This new method of energetic manipulation in a conjugated polymer paves the way for selective synthesis of polymers with electronically active spirocycles for future use. Conjugated system ; Polymer ; Heteroatom ; Materials science ; Nanotechnology ; Smart polymer ; Absorption (acoustics) ; Combinatorial chemistry ; Chemistry ; Organic chemistry ; Ring (chemistry) Luminescence and Fluorescent Materials ; Organic Electronics and Photovoltaics ; Conducting polymers and applications
Authors: Andreea Gheorghe
Source: UvA-DARE (University of Amsterdam) (article, 2020-01-01)
Field: Chemistry — Inorganic Chemistry

Critical factors in tuning the architecture and properties of metal-organic frameworks Metal-organic frameworks (MOFs) are porous crystalline materials that allow fine-tuning of their structural and chemical properties towards specific applications. Among them, the material known as MOF-74 has a large surface area and high density of Lewis acid sites, enabling the strong binding of CO2 or molecules with donor atoms, which act as Lewis bases. This thesis discusses the role of donor chiral molecules in the synthesis of chiral Zn-MOF-74 materials and the impact for catalytic as well as sensing applications. Chapter 1 gives an overview of the synthetic strategies used for obtaining chiral MOFs and their application in asymmetric catalysis. Chapter 2 demonstrates that cinchona alkaloids act as coordination modulators in the crystallisation process of Zn-MOF-74. It also highlights the role of the solvent in the formation of supramolecular isomers and their transformation to the most stable isomer. In chapter 3, the formation of defects and the pore blocking effect that arise from the post-synthetic modification of Zn-MOF-74 with L- or D-proline, are proven using complementary spectroscopic characterisation techniques as well as theoretical molecular simulations. Chapter 4 discusses the influence of chiral additives and solvents in the crystallisation of isoreticular Zn-MOF-74. Finally, chapter 5 demonstrates the suitability of Zn-MOF-74 for CO2 sensing at ambient conditions. Due to its selective CO2 adsorption and high proton conductivity, an impedance sensor based on Zn-MOF-74 showed fast response by changing the humidity and CO2 concentration. Lewis acids and bases ; Metal-organic framework ; Molecule ; Catalysis ; Supramolecular chemistry ; Crystallization ; Adsorption ; Nanotechnology ; Chemistry ; Combinatorial chemistry ; Porosity ; Materials science ; Chemical engineering ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; X-ray Diffraction in Crystallography ; Zeolite Catalysis and Synthesis
Authors: Marius Wehner
Source:  (article, 2020-09-11)
Field: Chemistry — Spectroscopy

Supramolecular Polymorphism in Homo- and Heterochiral Supramolecular Polymerizations The aim of the first part of this thesis was to investigate (R,R)-PBI as a model system for polymorphism at its origin by a supramolecular approach. The pathway complexity of (R,R)-PBI was fine-tuned by experimental parameters such as solvent, temperature and concentration to make several supramolecular polymorphs accessible. Mechanistic and quantum chemical studies on the kinetics and thermodynamics of the supramolecular polymerization of (R,R)-PBI were conducted to shed light on the initial stages of polymorphism. The second part of this work deals with mechanistic investigations on the supramolecular polymerization of the racemic mixture of (R,R)- and (S,S)-PBI with regard to homochiral and heterochiral aggregation leading to conglomerates and a racemic supramolecular polymer, respectively. Supramolecular chemistry ; Supramolecular polymers ; Polymerization ; Polymorphism (computer science) ; Chemistry ; Kinetics ; Supramolecular assembly ; Enantiomer ; Polymer ; Polymer chemistry ; Stereochemistry ; Crystallography ; Organic chemistry ; Crystal structure Analytical Chemistry and Chromatography ; Advanced Polymer Synthesis and Characterization ; Photopolymerization techniques and applications
Authors: Jinhai Mao | Milovanović, Slaviša P. | Anđelković, Miša | Lai, Xinyuan | Cao, Yang | Watanabe, Kenji | Taniguchi, Takashi | Covaci, Lucian | Peeters, Francois M. | Geim, Andre K. | Jiang, Yuhang | Andrei, Eva Y.
Source: RePEc: Research Papers in Economics (article, 2020-06-01)
Field: Materials Science — Materials Chemistry

Evidence of Flat Bands and Correlated States in Buckled Graphene Superlattices Two-dimensional atomic crystals can radically change their properties in response to external influences such as substrate orientation or strain, resulting in essentially new materials in terms of the electronic structure. A striking example is the creation of flat-bands in bilayer-graphene for certain 'magic' twist-angles between the orientations of the two layers. The quenched kinetic-energy in these flat-bands promotes electron-electron interactions and facilitates the emergence of strongly-correlated phases such as superconductivity and correlated-insulators. However, the exquisite fine-tuning required for finding the magic-angle where flat-bands appear in twisted-bilayer graphene, poses challenges to fabrication and scalability. Here we present an alternative route to creating flat-bands that does not involve fine tuning. Using scanning tunneling microscopy and spectroscopy, together with numerical simulations, we demonstrate that graphene monolayers placed on an atomically-flat substrate can be forced to undergo a buckling-transition, resulting in a periodically modulated pseudo-magnetic field, which in turn creates a post-graphene material with flat electronic bands. Bringing the Fermi-level into these flat-bands by electrostatic doping, we observe a pseudogap-like depletion in the density-of-states, which signals the emergence of a correlated-state. The described approach of 2D crystal buckling offers a strategy for creating other superlattice systems and, in particular, for exploring interaction phenomena characteristic of flat-bands. Superlattice ; Graphene ; Condensed matter physics ; Materials science ; Physics ; Nanotechnology Graphene research and applications