gebhart/patrepeval huggingface dataset:
Communication between subunits critical to DNA binding by hexameric helicase of bacteriophage T7 (2008)

The DNA helicase encoded by bacteriophage T7 consists of six identical subunits that form a ring through which the DNA passes. Binding of ssDNA is a prior step to translocation and unwinding of DNA by the helicase. Arg-493 is located at a conserved structural motif within the interior cavity of the helicase and plays an important role in DNA binding. Replacement of Arg-493 with lysine or histidine reduces the ability of the helicase to bind DNA, hydrolyze dTTP, and unwind dsDNA. In contrast, replacement of Arg-493 with glutamine abolishes these activities, suggesting that positive charge at the position is essential. Based on the crystallographic structure of the helicase, Asp-468 is in the range to form a hydrogen bonding with Arg-493 on the adjacent subunit. In vivo complementation results indicate that an interaction between Asp-468 and Arg-493 is critical for a functional helicase and those residues can be swapped without losing the helicase activity. This study suggests that hydrogen bonding between Arg-493 and Asp-468 from adjacent subunits is critical for DNA binding ability of the T7 hexameric helicase.
Cellobiose dehydrogenase functionalized urinary catheter as novel antibiofilm system (2015)

Urinary catheters expose patients to a high risk of acquiring nosocomial infections. To prevent this risk of infection, cellobiose dehydrogenase (CDH), an antimicrobial enzyme able to use various oligosaccharides as electron donors to produce hydrogen peroxide using oxygen as an electron acceptor, was covalently grafted onto plasma-activated urinary polydimethylsiloxane (PDMS) catheter surfaces. Successful immobilization of CDH on PDMS was confirmed by Fourier transformed-infrared spectrometry and production of H2 O2 . The CDH functionalized PDMS surfaces reduced the amount of viable Staphylococcus aureus by 60%, total biomass deposited on the surface by 30% and 70% of biofilm formation. The immobilized CDH was relatively stable in artificial urine over 16 days, retaining 20% of its initial activity. The CDH coated PDMS surface did not affect the growth and physiology of HEK 239 and RAW 264,7 mammalian cells. Therefore this new CDH functionalized catheter system shows great potential for solving the current problems associated with urinary catheters. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 104B: 1448-1456, 2016.
The Basis for Adhesive Bond Design (2012)

No AccessAdhesion and Adhesives TechnologyJun 2012The Basis for Adhesive Bond DesignAlphonsus V. PociusAlphonsus V. Pociushttps://doi.org/10.3139/9783446431775.013SectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF key 'share (en)' returned an object instead of string.FacebookTwitterEmailLinkedIn previous chapternext chapter FiguresReferencesRelatedDetails 2012Pages: 337-352Print ISBN: 978-3-446-42748-8eISBN: 978-3-446-43177-5 Copyright & Permissions© 2012 Carl Hanser Verlag GmbH & Co. KGPDF downloadLoading ...
Supplemental Methods, Figures 1 - 12, Tables 1 - 2, 4 from A Chemical Genetics Approach for the Functional Assessment of Novel Cancer Genes (2023)

&lt;p&gt;Supplemental Figure 1. Efficient knockâ€�in of DDâ€�domain into the endogenous p53 locus by TALENs in HCT116 cells. Supplemental Figure 2. PCR verification of Degronâ€�KI clones. Supplemental Figure 3. Immunofluorescence staining of Degronâ€�KI cells. Supplemental Figure 4. Quantification of DD tagged proteins in the presence or absence of Shld. Supplemental Figure 5. Highly efficient Degronâ€�KI at the endogenous EZH2 locus by CRISPR in HCT116. Supplemental Figure 6. Assessment of the kinetics of DDâ€�EZH2 and DDâ€�SF3B1 depletion upon Shld withdrawal. Supplemental Figure 7. HCT116 (EZH2 wild type) cells are not sensitive to EZH2 inhibitor EI1. Supplemental Figure 8. RTâ€�PCR strategy to identify alleleâ€� specific DD tagging of mutant versus wildtype SF3B1. Supplemental Figure 9. UQCC and CRNDE exhibit an altered splice pattern in SF3B1 mutant uveal melanoma cell lines. Supplemental Figure 10. Shld has minimal effects on gene expression of parental Mel202 cells and Mel202 DDâ€�mutâ€�SF3B1. Supplemental Figure 11. Selective depletion of mutant SF3B1 in Mel202 Degronâ€�KI cells reversed the alternative splicing pattern of DYNLL1, SNRPN, TMEM14C, ABCC5, ZDHHC16, RBM18. Supplemental Figure 12. Selective depletion of mutant SF3B1 in Mel202 Degronâ€�KI cells by Shld withdrawal predominantly alters 3' splice sites but not 5' splice site selection. Supplemental Figure 13. Confirmation that the DD tag insertion occurred exclusively at the SF3B1 locus in Degronâ€�KI engineered Mel202 clones. Supplemental Table 1: Detailed genotypes of ESSâ€�1 Degronâ€�KI clones. Supplemental Table 2: Detailed genotypes of Mel202 Degronâ€�KI clones. depletion using MATS. Supplemental Table 4: Comparison of the alternatively spliced genes identified in this study with genes reported in prior reports (5).&lt;/p&gt;
Heteropoly-13-Palladates(II) [PdII13(AsVPh)8O32]6− and [PdII13SeIV8O32]6− (2009)

Two discrete anionic palladium(II)-oxo clusters have been prepared: [Pd(13)(As(V)Ph)(8)O(32)](6-) (1) and [Pd(13)Se(IV)(8)O(32)](6-) (2) were synthesized in one-pot self-assembly reactions of Pd(OAc)(2) with PhAsO(3)H(2) and SeO(2) and characterized by single-crystal X-ray analysis, IR, thermogravimetric analysis, elemental analysis, magnetic and electron paramagnetic resonance measurements, and electrochemistry.
Preclinical development and qualification of ZFN-mediated CCR5 disruption in human hematopoietic stem/progenitor cells (2016)

Gene therapy for HIV-1 infection is a promising alternative to lifelong combination antiviral drug treatment. Chemokine receptor 5 (CCR5) is the coreceptor required for R5-tropic HIV-1 infection of human cells. Deletion of CCR5 renders cells resistant to R5-tropic HIV-1 infection, and the potential for cure has been shown through allogeneic stem cell transplantation with naturally occurring homozygous deletion of CCR5 in donor hematopoietic stem/progenitor cells (HSPC). The requirement for HLA-matched HSPC bearing homozygous CCR5 deletions prohibits widespread application of this approach. Thus, a strategy to disrupt CCR5 genomic sequences in HSPC using zinc finger nucleases was developed. Following discussions with regulatory agencies, we conducted IND-enabling preclinical <i>in vitro</i> and <i>in vivo</i> testing to demonstrate the feasibility and (preclinical) safety of zinc finger nucleases-based CCR5 disruption in HSPC. We report here the clinical-scale manufacturing process necessary to deliver CCR5-specific zinc finger nucleases mRNA to HSPC using electroporation and the preclinical safety data. Our results demonstrate effective biallelic CCR5 disruption in up to 72.9% of modified colony forming units from adult mobilized HSPC with maintenance of hematopoietic potential <i>in vitro</i> and <i>in vivo</i>. Tumorigenicity studies demonstrated initial product safety; further safety and feasibility studies are ongoing in subjects infected with HIV-1 (NCT02500849@clinicaltrials.gov).
Growth requirements of calf lens epithelium in culture (1978)

The in vitro life span and rate of growth of calf lens cells cultured in serum-supplemented 199 medium can be markedly increased by growing the cells with a layer of mitomycin -killed 3T6 feeders. In the absence of feeders, the epithelial cells are partially blocked in the S period of the cell cycle but show a normal distribution of cells in G1 and G2 when grown with fibroblasts. Increased growth rates and division potential can also be achieved by growing the lens in 199 medium containing 10(-5) M thymidine, and cells grown under these conditions show a normal growth cycle. Our results suggest that lens epithelial cells cultured in medium 199 show a deficient endogenous synthesis of thymidylic acid, and fibroblast feeders or exogenously added thymidine enable them to overcome this deficiency. When grown in the presenct of 10(-5) M thymidine, the lens epithelial cells show a very low serum requirement for cell division in short term culture.
Smart multispectral image acquisition and multi-channel image processing with programmable system on chip devices (2019)

Through the acquisition and processing of several spectral channels within the multispectral data, the demands on signal processing and data handling increase enormously. With the help of intelligent signal pre-processing on programmable system on chip platforms (pSoC), captured data can be corrected and evaluated directly after image acquisition. PSoC combine the advantages of freely programmable logic (FPGA) and sequential processor systems (ARM technology) and significantly increase the integration density of embedded image processing systems. However, the design effort for these systems is increasing strongly, so that hardware/software co-design approaches must be used for implementation. The paper covers the design methodology, the implementation and the evaluation of multichannel acquisition systems using multispectral image sensors as an example.
Directional emission from dye-functionalized plasmonic DNA superlattice microcavities (2017)

Three-dimensional plasmonic superlattice microcavities, made from programmable atom equivalents comprising gold nanoparticles functionalized with DNA, are used as a testbed to study directional light emission. DNA-guided nanoparticle colloidal crystallization allows for the formation of micrometer-scale single-crystal body-centered cubic gold nanoparticle superlattices, with dye molecules coupled to the DNA strands that link the particles together, in the form of a rhombic dodecahedron. Encapsulation in silica allows one to create robust architectures with the plasmonically active particles and dye molecules fixed in space. At the micrometer scale, the anisotropic rhombic dodecahedron crystal habit couples with photonic modes to give directional light emission. At the nanoscale, the interaction between the dye dipoles and surface plasmons can be finely tuned by coupling the dye molecules to specific sites of the DNA particle-linker strands, thereby modulating dye-nanoparticle distance (three different positions are studied). The ability to control dye position with subnanometer precision allows one to systematically tune plasmon-excition interaction strength and decay lifetime, the results of which have been supported by electrodynamics calculations that span length scales from nanometers to micrometers. The unique ability to control surface plasmon/exciton interactions within such superlattice microcavities will catalyze studies involving quantum optics, plasmon laser physics, strong coupling, and nonlinear phenomena.
Methacrylate Star Synthesis by GTP (1991)

Abstract All process conditions were picked to minimize the back-biting termination reaction so the maximum level of living arm could be carried into the core-forming step. Major contributors to control of termination were: 1. Using 0.2% (mole basis) of catalyst on initiator instead of higher concentrations. Within the constraints defined below, this produces a robust process that is insensitive to minor changes in materials, temperatures, and rates of addition. 2. Minimizing the time between arm formation and core formation. Polymerization of arm monomethacrylate to about 96 to 98% before core formation was the aim because conversion to &gt;99% would have allowed too much time for termination to proceed. 3. Adding core-forming monomer (ethylene glycol dimethacrylate) in about 5 min to keep monomer concentration high in this step. Faster add times may not be desirable because of mixing difficulties in this extremely fast polymerization. 4. Reaction solvent mixture containing 50% tetrahydrofuran. This allowed the reflux temperature to be about 85°C. 5. Keeping monomer concentration high in the arm-forming step by starting the polymerization with half of the monomer in the reactor. This forced the polymerization past the trimer stage, where termination is fastest. 6. Starting the reaction at room temperature so the exotherm could be dissipated by the heat capacity of the system. Two lots of trimethylsiloxyethyl methacrylate used to introduce hydroxyl groups into the product (after unblocking) gave different rates of polymerization, with one lot reaching the core-forming step in about half the time of the other. The monomer lot with the higher reactivity also led to higher levels of free arm. Stars made at high (2.0%) catalyst levels were quite unstable to molecular weight and viscosity increase. Mechanistic studies show that the increase is probably because of star/ star free-radical methacrylate polymerization involving pendant residual methacrylate unsaturation from the core-forming step. Stars made under the recommended conditions using 0.2% catalyst and the above process steps are probably stable enough for commercial use.
ChemInform Abstract: RK. MIT CYCLOBUTENDIONEN 19. MITT. RINGOEFFNUNG DER DIARYL‐CYCLOBUTENDIONE MIT GRIGNARD‐VERBINDUNGEN (1971)

Abstract Die durch Reaktion von 3,3,4,4‐Tetrafluor‐1,2‐dichlor‐cyclobuten‐(1) mit entsprechenden Aryl‐Li‐Verbindungen und darauffolgender Oxidation erhaltenen Cyclobutendione (I) reagieren mit den Aryl‐Mg‐bromiden (II) unter Bildung der cis‐Diaroylstilbene (III) (Ausbeute 40%) und der säulenchromatographisch isolierten Butandione (IV) (30%) und Furane (V) (5%).
Solvation Structure of Uracil in Ionic Liquids (2016)

The local solvation environment of uracil dissolved in the ionic liquid 1-ethyl-3-methylimidazolium acetate has been studied using neutron diffraction techniques. At solvent:solute (ionic liquid:uracil) ratios of 3:1 and 2:1, little perturbation of the ion-ion correlations compared to those of the neat ionic liquid are observed. We find that solvation of the uracil is driven predominantly by the acetate anion of the solvent. While short distance correlations exist between uracil and the imidazolium cation, the geometry of these contacts suggest that they cannot be considered as hydrogen bonds, in contrast to other studies by Araújo et al. (J. M. Araújo, A. B. Pereiro, J. N. Canongia-Lopes, L. P. Rebelo, I. M. Marrucho, J. Phys. Chem. B 2013, 117, 4109-4120). Nevertheless, this combination of interactions of the solute with both the cation and anion components of the solvents helps explain the high solubility of the nucleobase in this media. In addition, favourable uracil-uracil contacts are observed, of similar magnitude to those between cation and uracil, and are also likely to aid dissolution.
The impact of molecular targets in cancer drug development: major hurdles and future strategies (2012)

The last decades were characterized by enormous technological advances resulting in a better understanding of disease pathologies and improvement of treatment strategies. The development of targeted drugs, whose beginning can be traced back to Paul Ehrlich's theory of the 'magic bullet' approximately 100 years ago, is today widely appraised as a promising strategy to combat benign, as well as malignant, diseases. Over 40 years after US President Nixon declared the 'war on cancer', treatment outcome, especially of solid tumors in the advanced stages of disease, still lies far behind expectations. In this perspective article, the authors discuss the recent development of targeted cancer drugs and identify major hurdles. The authors further highlight future strategies that might improve and accelerate the drug-development process.
Understanding filamentary growth in electrochemical metallization memory cells using kinetic Monte Carlo simulations (2015)

We report on a 2D kinetic Monte Carlo model that describes the resistive switching in electrochemical metallization cells. To simulate the switching process, we consider several different processes on the atomic scale: electron-transfer reactions at the boundaries, ion migration, adsorption/desorption from/to interfaces, surface diffusion and nucleation. These processes result in a growth/dissolution of a metallic filament within an insulating matrix. In addition, the model includes electron tunneling between the growing filament and the counter electrode, which allows for simulating multilevel switching. It is shown that the simulation model can reproduce the reported switching kinetics, switching variability and multilevel capabilities of ECM devices. As a major result, the influence of mechanical stress working on the host matrix due to the filamentary growth is investigated. It is demonstrated that the size and shape of the filament depend on the Young's modulus of the insulating matrix. For high values a wire-like structure evolves, whereas the shape is dendritic if the Young's modulus is negligible.
Impact of $Al_2O_3$ Passivation on the Photovoltaic Performance of\n Vertical $WSe_2$ Schottky Junction Solar Cells (2020)

Transition metal dichalcogenide (TMD) materials have emerged as promising\ncandidates for thin film solar cells due to their wide bandgap range across the\nvisible wavelengths, high absorption coefficient and ease of integration with\nboth arbitrary substrates as well as conventional semiconductor technologies.\nHowever, reported TMD-based solar cells suffer from relatively low external\nquantum efficiencies (EQE) and low open circuit voltage due to unoptimized\ndesign and device fabrication. This paper studies $Pt/WSe_2$ vertical Schottky\njunction solar cells with various $WSe_2$ thicknesses in order to find the\noptimum absorber thickness.Also, we show that the photovoltaic performance can\nbe improved via $Al_2O_3$ passivation which increases the EQE by up to 29.5% at\n410 nm wavelength incident light. The overall resulting short circuit current\nimproves through antireflection coating, surface doping, and surface trap\npassivation effects. Thanks to the ${Al_2O_3}$ coating, this work demonstrates\na device with open circuit voltage ($V_{OC}$) of 380 mV and short circuit\ncurrent density ($J_{SC}$) of 10.7 $mA/cm^2$. Finally, the impact of Schottky\nbarrier height inhomogeneity at the $Pt/WSe_2$ contact is investigated as a\nsource of open circuit voltage lowering in these devices\n
Nondoped-type white organic electroluminescent devices utilizing complementary color and exciton diffusion (2002)

We fabricated nondoped white organic electroluminescent devices using vacuum-deposited thin films of blue-emitting 4,4′-bis[N-1-napthyl-N-phenyl-amino]biphenyl (α-NPD) and orange-emitting 4-(dicyanomethylene)-2-metyl-6-(p-dimethyl aminostyryl)-4H-pyran (DCM), a hole-blocking layer of 2-(4-biphenyl)-5-(p-tert-butylphenyl)-1,3,4-oxadiazole (tBu-PBD) and electron-transporting tris(8-quinolinolato) aluminum (III). Excitons formed at the α-NPD/tBu-PBD interface sequentially transfer their energy to α-NPD via the Förster mechanism. The exciton is captured by an ultrathin DCM layer located within the pure α-NPD layer. The position of the DCM determines the device spectrum, and enables a white emission to be achieved. The spectrum is not sensitive to the voltage applied, and the devices show maximum luminance of about 1000 cd/m2.
Tabletop Coherent Diffractive Microscopy with Soft X-rays from High Harmonic Generation at 13.5 nm (2009)

We demonstrate lensless diffractive microscopy with 92nm resolution using 13.5nm light from high harmonic generation. Fast image retrieval with Fourier transform holography is shown, and we present paths to refining the images to higher resolution.
Plant and animal profilins are functionally equivalent and stabilize microfilaments in living animal cells (1996)

We have analyzed the degree of functional similarity between birth and mammalian profilins, two members of the profilin family which show only a moderate sequence homology (22%) in living animal cells. The plant profilin, derived from birch pollen, was stably expressed in BHK-21 cells. Plant and endogenous profilin synthesis and cellular distribution were monitored by specific monoclonal antibodies. Quantitation of profilin and actin on calibrated immunoblots showed that two stable clones contained in total 1.4 and 2.0 times as much profilin as the parental cells. Using double fluorescence and confocal laser scanning microscopy, it was seen that the endogenous and the plant profilin colocalized with dynamic microfilaments, in particular with F-actin-rich foci and cortical microfilament webs of spreading cells, with dynamic microfilament bundles induced by serum deprival, and with cytochalasin D- and latrunculin-induced transient F-actin aggregates. The increase in the overall profilin concentration correlated with a significantly higher resistance of actin filaments to these drugs. Our data indicate that even profilins of highly distant evolutionary origin can functionally substitute for each other and support the hypothesis that in animal cells, profilins are engaged in regulating either the stability or the kinetic properties of actin filaments.
Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data (2013)

The Genia Event (GE) extraction task of the BioNLP Shared Task addresses the extraction of biomedical events from the natural language text of the published literature. In our submission, we modified an existing system for learning of event patterns via dependency parse subgraphs to utilise a more accurate parser and significantly more, but noisier, training data. We explore the impact of these two aspects of the system and conclude that the change in parser limits recall to an extent that cannot be offset by the large quantities of training data. However, our extensions of the system to extract modification events shows promise. 1
High efficiency and low efficiency roll off in white phosphorescent organic light-emitting diodes by managing host structures (2008)

High efficiency phosphorescent white organic light-emitting diodes with little efficiency roll off were developed by managing the charge transport properties of the host materials. The emitting layers were stacked at a sequence of red/blue/green from the hole transport layer side and charge injection could be easily controlled by changing the host materials in the red and green emitting layers. A high quantum efficiency of 13% was obtained at a luminance of 1000cd∕m2. In addition, the quantum efficiency of the white device at low luminance was maintained up to 10000cd∕m2 without any decrease.
Structural Basis of the Diversity of Adrenergic Receptors (2019)

Adrenergic receptors are highly homologous while at the same time display a wide diversity of ligand and G-protein binding, and understanding this diversity is key for designing selective or biased drugs for them. Here, we determine two crystal structures of the α<sub>2A</sub> adrenergic receptor (α<sub>2A</sub>AR) in complex with a partial agonist and an antagonist. Key non-conserved residues from the ligand-binding pocket (Phe<sup>7.39</sup> and Tyr<sup>6.55</sup>) to G-protein coupling region (Ile<sup>34.51</sup> and Lys<sup>34.56</sup>) are discovered to play a key role in the interplay between partial agonism and biased signaling of α<sub>2A</sub>AR, which provides insights into the diversity of ligand binding and G-protein coupling preference of adrenergic receptors and lays the foundation for the discovery of next-generation drugs targeting these receptors.