jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ezgi ERSÖZ | Rehime Yapar | Burak Çelik | Mehmet Korkmaz
Source: Eastern Journal Of Medicine (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Evaluation of Apoptotic and Autophagic Effects of Thioridazine in Monolayer and Spheroid Cell Cultures Glioblastoma (GBM) is the most frequently seen brain tumor in adults.It is clear that new therapeutic agents are needed in this area.Spheroid cell cultures have advantages on imitating in vivo environment.Therefore, we investigated apoptotic and autophagic effects of Thioridazine (THZ) which is a potential anti-cancer agent on GBM cell lines, T98G and U-87 MG, comparatively in monolayer and spheroid cell cultures.The cytotoxic effect of THZ on cells was evaluated by MTT method.Besides, apoptotic and autophagic effects of THZ were determined by Annexin V and LC-3 antibody based methods.Validation performed also by assessment of apoptosis and autophagy with specific inhibitors.The analysis has revealed that IC 50 values at 24 h were 12,67 M (T98G) and 12.80 M (U-87 MG) in monolayer cell culture, 29.30 M (T98G) and 28.68 M (U-87 MG) in spheroid cell culture.While apoptotic cell rate was determined at 24 h approximate 15% in both cell lines and cell cultures, autophagy induction rate was increased by 6.5-(T98G) and 5.6-(U-87 MG) fold in monolayer cell culture and by 3.3-(T98G) and 4.5-(U-87 MG) fold in spheroid cell culture.In our study THZ stimulates mostly autophagy rather than apoptosis.In addition, it can be suggested that in vitro cytotoxicity studies should perform with not only monolayer cell cultures but also with spheroid cell cultures for obtaining in vivo-like data.When all the evaluations are considered, THZ might be thought as a potential chemotherapeutic agent in the treatment of GBM. Spheroid ; Autophagy ; Thioridazine ; Medicine ; Apoptosis ; Cell ; Cell biology ; Cancer research ; Cell culture ; Pharmacology ; Genetics ; Biology Synthesis and Characterization of Heterocyclic Compounds ; Click Chemistry and Applications ; RNA Interference and Gene Delivery
Authors: Andres Tellez-Mora | Xu He | Éric Bousquet | Ludger Wirtz | A. Romero
Source: Research Square (preprint, 2023-08-17)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Systematic determination of a material's magnetic ground state from first principles Ground state ; State (computer science) ; Computer science ; Physics ; Algorithm ; Atomic physics Magnetic Properties and Applications ; Magnetic and transport properties of perovskites and related materials ; Magnetic properties of thin films
Authors: Shengbo Wang | Andrew Collins | Ananth Prakash | Silvie Fexová | Irene Papatheodorou | Andrew R. Jones | Juan Antonio Vizcaíno
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-11-10)
Field: Chemistry — Spectroscopy

Integrated Proteomics analysis of baseline protein expression in pig tissues Abstract The availability of an increasingly large amount of public proteomics datasets presents an opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biological conditions. Sus scrofa , the domestic pig, is a model organism relevant for food production and for human biomedical research. Here we reanalyzed 14 public proteomics datasets from the PRIDE database coming from pig tissues to assess baseline (without any biological perturbation) protein abundance in 14 organs, encompassing a total of 20 healthy tissues from 128 samples. The analysis involved the quantification of protein abundance in 599 mass spectrometry runs. We compared protein expression patterns among different pig organs and examined the distribution of proteins across these organs. Then, we studied how protein abundances compared across different datasets and studied the tissue specificity of the detected proteins. Of particular interest, we conducted a comparative analysis of protein expression between pig and human tissues, revealing a high degree of correlation in protein expression among orthologs, particularly in brain, kidney, heart, and liver samples. We have integrated the protein expression results into the Expression Atlas resource for easy access and visualisation of the protein expression data individually or alongside gene expression data. Human Protein Atlas ; Proteomics ; Protein expression ; Biology ; Computational biology ; Organism ; Gene expression ; Gene expression profiling ; Gene ; Genetics Advanced Proteomics Techniques and Applications ; Meat and Animal Product Quality ; Metabolomics and Mass Spectrometry Studies
Authors: Sandeep Aryal | Deepti Anand | Hongzhan Huang | Ashok P. Reddy | Phillip A. Wilmarth | Larry L. David | Salil A. Lachke
Source: Research Square (preprint, 2023-03-17)
Field: Chemistry — Spectroscopy

Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ³2.5 average spectral counts, ³2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information and facilitate eye gene discovery. Proteome ; Biology ; Retinal pigment epithelium ; Retina ; Proteomics ; Computational biology ; Transcriptome ; In silico ; Gene expression profiling ; Gene ; Bioinformatics ; Genetics ; Gene expression ; Neuroscience Advanced Proteomics Techniques and Applications ; Retinal Development and Disorders ; S100 Proteins and Annexins
Authors: Paulina Jureczko | Jozef Haniš | Junior, Paulo E. Faria | Martin Gmitra | Marcin Kurpas
Source: arXiv (Cornell University) (preprint, 2023-02-06)
Field: Chemistry — Inorganic Chemistry

Probing type-II Ising pairing using the spin-mixing parameter The immunity of Ising superconductors to external magnetic fields originates from a spin locking of the paired electrons to an intrinsic Zeeman-like field. The spin-momentum locking in non-centrosymmetric crystalline materials leads to type-I Ising pairing in which the direction of the intrinsic field can be deduced from the spin expectation values. Conversely, in centrosymmetric crystals the electron spins locked to the orbitals can form Ising type-II pairs consisting of spin-orbit split doublets. Due to time-reversal symmetry, the doublets are spin degenerate, making it difficult to read the spin polarization of bands and the direction of spin-orbit fields. Here we present an efficient approach to determine the direction of the intrinsic field using the spin-mixing parameter $b^2$. Using first principles calculations based on the density functional theory, we study monolayer transition metal dichalcogenide superconductors PdTe$_2$, NbTe$_2$, and TiSe$_2$ with the 1T structure. We calculate $b^2$ for individual Fermi pockets and provide a general picture of possible Ising type-II pairing within the full Brillouin zone. In order to complement our first principles results, we use group theory to provide a detailed picture of spin-orbit coupling and spin mixing in the relevant bands forming Fermi pockets. We demonstrate that contrary to the anticipated effects of spin-orbit locking, not every spin-orbit split spin doublet actively participates in Ising pairing. Finally, by connecting the spin-mixing parameter $b^2$ with the intrinsic out-of-plane Zeeman field we estimate the upper in-plane critical magnetic field. Condensed matter physics ; Ising model ; Zeeman effect ; Physics ; Pairing ; Spin (aerodynamics) ; Spins ; Degenerate energy levels ; Superconductivity ; Quantum mechanics ; Magnetic field Inorganic Chemistry and Materials ; Magnetic and transport properties of perovskites and related materials ; Electronic and Structural Properties of Oxides
Authors: Wenxin Hua | Rui Sun | Xiaoyan Wang | Yunyun Zhang | Jiaxing Li | Ri Qiu | Yu Gao
Source: Research Square (preprint, 2023-10-19)
Field: Materials Science — Materials Chemistry

Corrosion of Q235 carbon steel induced by sulfate-reducing bacteria in groundwater: corrosion behavior, corrosion product and microbial community structure Abstract Microbiologically influenced corrosion (MIC) is one of the reasons leading to the service failure of pipelines buried in the soil. To investigate the effect of sulfate-reducing bacteria (SRB) on the corrosion behavior of Q235 carbon steel in groundwater, a hanging plate test was carried out and the SRB was characterized by electrochemical methods, surface analysis, and biological analysis. In addition, a group of blank experiments was used as a control. The results showed that SRB continued to grow and reproduce in groundwater without lacking a carbon source for 14d to maintain life activities. The community structure has changed after corrosion, and the dominant species of SRB has changed from Desulfovibrio to Desulfosporosinus . During the whole growth cycle, the electrochemical results demonstrated that the impedance of the carbon steel surface forming a biofilm was 1 order of magnitude higher than that of other periods, and the formed ferrous sulfide layer also hindered the occurrence of corrosion. In comparison to the condition without SRB, the inclusion of SRB results in reduced weight loss. The average weight loss with SRB is 0.01389 g, whereas the average weight loss without SRB is 0.03956 g. However, the 3D topography indicated that the surface of carbon steel was more uneven and pits were increased with SRB. Altogether these results implied that the growth of SRB makes the corrosion process of Q235 carbon steel more complicated. Corrosion ; Sulfate-reducing bacteria ; Carbon steel ; Metallurgy ; Mackinawite ; Materials science ; Ferrous ; Pitting corrosion ; Sulfide ; Sulfate ; Electrochemistry ; Carbon fibers ; Groundwater ; Chemistry ; Composite material ; Geology ; Geotechnical engineering ; Electrode Corrosion Behavior and Inhibition ; Concrete Corrosion and Durability ; Hydrogen embrittlement and corrosion behaviors in metals
Authors: Christopher A. Haynes | Theodore R. Keppel | Betlehem Mekonnen | Sarah Osman | Yu Zhou | Adrian R. Woolfitt | Jakub Baudys | John R. Barr | Dongxia Wang
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-06-15)
Field: Chemistry — Spectroscopy

Inclusion of glycopeptides in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike ectodomain provides in-creased sequence coverage Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a protein’s conformational dynamics across varied states, such as heat-denatured vs. native protein structures, localizing regions that are specifically affected by such conditional changes. Maximizing protein sequence coverage provides high confidence that regions of interest were located by HDX-MS, but one challenge for complete sequence coverage is N-glycosylation sites. The deuteration of glycopeptides has not always been identified in previous reports of HDX-MS analyses, causing significant sequence coverage gaps in heavily glycosylated proteins and uncertainty in structural dynamics in many regions throughout a glycoprotein. We report HDX-MS analysis of the SARS-CoV-2 spike protein ectodomain in its trimeric pre-fusion form, which has 22 predicted N-glycosylation sites per monomer, with and without heat treatment. We identified glycopeptides and calculated their isotopic mass shifts from deuteration. Inclusion of the deu-terated glycopeptides increased sequence coverage of spike ectodomain from 76% to 84%, demonstrated that glycopeptides had been deuterated, and improved confidence in results localizing structural re-arrangements. Inclusion of deuterated glycopeptides improves the analysis of the conformational dynamics of glycoproteins such as viral surface antigens and cellular receptors. Abstract Figure Ectodomain ; Chemistry ; Hydrogen–deuterium exchange ; Sequence (biology) ; Glycopeptide ; Mass spectrometry ; Glycosylation ; Biochemistry ; Chromatography ; Receptor Mass Spectrometry Techniques and Applications ; RNA and protein synthesis mechanisms ; Advanced Proteomics Techniques and Applications
Authors: Christopher A. Haynes | Theodore R. Keppel | Betlehem Mekonnen | Sarah H. Osman | Yu Zhou | Adrian R. Woolfitt | Jakub Baudys | John R. Barr | Dawei Wang
Source:  (preprint, 2023-09-15)
Field: Chemistry — Spectroscopy

Inclusion of deuterated glycopeptides provides increased sequence coverage in hydrogen/deuterium exchange mass spectrometry analysis of SARS-CoV-2 spike glycoprotein Rationale. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) can provide precise analysis of a protein’s conformational dynamics across varied states, such as heat-denatured vs. native protein structures, localizing regions that are specifically affected by such conditional changes. Maximizing protein sequence coverage provides high confidence that regions of interest were located by HDX-MS, but one challenge for complete sequence coverage is N-glycosylation sites. The deuteration of peptides post-translationally modified by asparagine-bound glycans (glycopeptides) has not always been identified in previous reports of HDX-MS analyses, causing significant sequence coverage gaps in heavily glycosylated proteins and uncertainty in structural dynamics in many regions throughout a glycoprotein. Methods . We detected deuterated glycopeptides with a Tribrid Orbitrap Eclipse mass spectrometer performing data-dependent acquisition. An MS scan was used to identify precursor ions, if high-energy collision-induced dissociation (HCD) MS/MS of the precursor indicated oxonium ions diagnostic for complex glycans then electron transfer low-energy collision-induced dissociation (EThcD) MS/MS scans of the precursor identified the modified asparagine residue and the glycan’s mass. As in traditional HDX-MS the identified glycopeptides were then analyzed at the MS level in samples labeled with D O. Results. We report HDX-MS analysis of the SARS-CoV-2 spike protein ectodomain in its trimeric pre-fusion form, which has 22 predicted N-glycosylation sites per monomer, with and without heat treatment. We identified glycopeptides and calculated their average isotopic mass shifts from deuteration. Inclusion of the deuterated glycopeptides increased sequence coverage of spike ectodomain from 76% to 84%, demonstrated that glycopeptides had been deuterated, and improved confidence in results localizing structural re-arrangements. Conclusion. Inclusion of deuterated glycopeptides improves the analysis of the conformational dynamics of glycoproteins such as viral surface antigens and cellular receptors. Chemistry ; Hydrogen–deuterium exchange ; Mass spectrometry ; Electron-transfer dissociation ; Glycan ; Asparagine ; Dissociation (chemistry) ; Tandem mass spectrometry ; Glycoprotein ; Chromatography ; Amino acid ; Biochemistry ; Organic chemistry Mass Spectrometry Techniques and Applications ; Influenza Virus Research Studies ; Advanced Proteomics Techniques and Applications
Authors: Miguel Herranz | Clara Pedrosa | Daniel Martínez-Fernández | Katerina Foteinopoulou | Nikos Ch. Karayiannis | Manuel Laso
Source: arXiv (Cornell University) (preprint, 2023-05-08)
Field: Chemistry — Organic Chemistry

Fine-Tuning of Colloidal Polymer Crystals by Molecular Simulation Through extensive molecular simulations we determine a phase diagram of attractive, flexible polymer chains in two and three dimensions. A surprisingly rich collection of distinct crystal morphologies appear, which can be finely tuned through the range of attraction. In three dimensions these include the face centered cubic, hexagonal close packed, simple hexagonal and body centered cubic crystals and the Frank-Kasper phase. A simple geometric model is proposed, based on the concept of cumulative neighbours of ideal crystals, which can accurately predict most of the observed structures and the corresponding transitions. The attraction range can thus be considered as an adjustable parameter for the design of colloidal polymer crystals with tailored morphologies. Phase diagram ; Materials science ; Cubic crystal system ; Polymer ; Colloidal crystal ; Ideal (ethics) ; Phase (matter) ; Chemical physics ; Crystal (programming language) ; Colloid ; Hexagonal crystal system ; Attraction ; Range (aeronautics) ; Simple (philosophy) ; Nanotechnology ; Crystallography ; Physics ; Chemistry ; Computer science ; Physical chemistry ; Composite material Advanced Polymer Synthesis and Characterization
Authors: Miguel Herranz Feito | Clara Pedrosa Cano | Daniel Martínez Fernández | Aikaterini Foteinopoulou | Nikos Ch. Karagiannis | Manuel Laso Carbajo
Source: UPM Digital Archive (Technical University of Madrid) (article, 2023-06-21)
Field: Materials Science — Materials Chemistry

Fine-tuning of colloidal polymer crystals by molecular simulation Through extensive molecular simulations we determine a phase diagram of attractive, fully flexible polymer chains in two and three dimensions. A rich collection of distinct crystal morphologies appear, which can be finely tuned through the range of attraction. In three dimensions these include the face-centered cubic, hexagonal close packed, simple hexagonal, and body-centered cubic crystals and the Frank-Kasper phase. In two dimensions the dominant structures are the triangular and square crystals. A simple geometric model is proposed, based on the concept of cumulative neighbors of ideal crystals, which can accurately predict most of the observed structures and the corresponding transitions. The attraction range can thus be considered as an adjustable parameter for the design of colloidal polymer crystals with tailored morphologies. Phase diagram ; Polymer ; Ideal (ethics) ; Colloidal crystal ; Colloid ; Square (algebra) ; Crystal (programming language) ; Phase (matter) ; Simple (philosophy) Block Copolymer Self-Assembly ; Material Dynamics and Properties ; Liquid Crystal Research Advancements
Authors: Ali Dabbous | Eloïse Colson | D. Chakravorty | Jean‐Marie Mouesca | Christian Lombard | Sylvain Caillat | Jean‐Luc Ravanat | Fabien Dubois | F. Dénès | Philippe Renaud | Vincent Maurel
Source: ChemRxiv (preprint, 2023-01-29)
Field: Chemistry — Organic Chemistry

Fine tuning of quantum dots photocatalysts for the synthesis of tropane alkaloid skeletons Several types of Quantum Dots (QDs) (CdS, CdSe and InP, as well as core-shell QDs such as type I InP-ZnS, quasi type-II CdSe-CdS and inverse type-I CdS-CdSe) were considered for generating α-aminoalkyl free radicals. The feasibility of the oxidation of the N-aryl amines and the generation of the desired radical was evidenced experimentally by quenching of the photoluminescence of the QDs and by testing a vinylation reaction using an alkenylsulfone radical trap. The QDs were tested in a radical [3+3]-annulation reaction giving access to tropane skeletons and that requires the completion of two consecutive catalytic cycles. Several QDs such as CdS core, CdSe core and inverted type I CdS-CdSe core-shell proved to be efficient photocatalysts for this reaction. Interestingly, the addition of a second shorter chain ligand to the QDs appeared to be essential to complete the second catalytic cycle and to obtain the desired bicyclic tropane derivatives. Finally, the scope of the [3+3]-annulation reaction was explored for the best performing QDs and isolated yields that compares well with classical iridium photocatalysis were obtained. Photocatalysis ; Quantum dot ; Chemistry ; Tropane ; Photochemistry ; Photoluminescence ; Ligand (biochemistry) ; Radical ; Catalysis ; Quenching (fluorescence) ; Combinatorial chemistry ; Materials science ; Nanotechnology ; Fluorescence ; Stereochemistry ; Organic chemistry ; Optoelectronics ; Physics Radical Photochemical Reactions
Authors: Luzia S. Germann | Elvio Carlino | A. Taurino | Oxana V. Magdysyuk | Dario Voinovich | Robert E. Dinnebier | Dejan-Krešimir Buč̌ar | Dritan Hasa
Source: Angewandte Chemie (article, 2023-01-09)
Field: Chemistry — Physical and Theoretical Chemistry

Modulating Thermal Properties of Polymers through Crystal Engineering Abstract Crystal engineering has exclusively focused on the development of advanced materials based on small organic molecules. We now demonstrate how the cocrystallization of a polymer yields a material with significantly enhanced thermal stability but equivalent mechanical flexibility. Isomorphous replacement of one of the cocrystal components enables the formation of solid solutions with melting points that can be readily fine‐tuned over a usefully wide temperature range. The results of this study credibly extend the scope of crystal engineering and cocrystallization from small molecules to polymers. Crystal engineering ; Cocrystal ; Polymer ; Materials science ; Thermal stability ; Molecule ; Molecular engineering ; Flexibility (engineering) ; Crystal (programming language) ; Melting point ; Thermal ; Crystal structure ; Small molecule ; Nanotechnology ; Chemistry ; Crystallography ; Organic chemistry ; Hydrogen bond ; Thermodynamics ; Composite material ; Computer science ; Physics Crystallography and molecular interactions ; Energetic Materials and Combustion ; Thermal and Kinetic Analysis
Authors: Soumyadeep Ghosh
Source: SSRN Electronic Journal (article, 2023-01-01)
Field: Chemistry — Organic Chemistry

Synthesis and Characterization of N,N Donor (ATIs) Ligands Characterization (materials science) ; Chemistry ; Combinatorial chemistry ; Stereochemistry ; Nanotechnology ; Materials science Organometallic Complex Synthesis and Catalysis ; Chemical Synthesis and Reactions ; Asymmetric Hydrogenation and Catalysis