gebhart/patrepeval huggingface dataset:
Laminin chain assembly by triple and double stranded coiled-coil structures. (1992)

We have previously provided evidence that laminin assembly occurs by the specific interaction of the alpha-helical domains of the A, B1, and B2 chains, located within the long arm of the molecule (Hunter, I., Schulthess, T., Bruch, M., Beck, K., and Engel, J. (1990) Eur. J. Biochem. 188, 205-211). Recent evidence for noncoordinate synthesis of the laminin chains, and in particular, the absence of the 400-kDa A chain from laminins produced by a number of cell types, has led us to examine the molecular mechanism of laminin assembly using the isolated A and B1-B2 chains of laminin fragment E8. E8A shows little tendency to self-associate, and when renatured from urea forms globular structures with little detectable alpha-helix. In contrast, E8B1-B2 renatures to form rod-like molecules, 30 nm in length. The rod-like structure, high alpha-helix content, and sharp thermal transition indicate that they are double stranded coiled coils. When mixed in equimolar amounts, E8A and E8B1-B2 renature to form molecules which are biochemically and ultrastructurally indistinguishable from native E8. If E8A and E8B1-B2 are renatured separately and mixed at a 1:1 molar ratio, they also form E8 molecules. These results suggest a mechanism of laminin assembly which involves the formation of a double coiled-coil B1-B2 intermediate with which the A chain subsequently interacts to form a triple coiled-coil laminin molecule. In addition, our results indicate that isoforms consisting of the B1 and B2 chains only would form stable "laminin-like" structures.
Secretin family (Class B) G protein‐coupled receptors – from molecular to clinical perspectives (2012)

Family B G protein-coupled receptors represent an important but under-researched group of receptors. This edition of the British Journal of Pharmacology considers the roles and pharmacology of a number of these receptors. Whilst common themes emerge, it is clear that more work is needed to understand the details of each receptor in order to properly exploit them therapeutically.
Pharmacokinetics, adverse effects and tolerability of a novel analogue of human pancreatic polypeptide, PP 1420 (2011)

Subcutaneous PP 1420 was well tolerated in healthy human subjects at single doses between 2-8 mg, with no tolerability issues arising. Where observed, adverse events were not serious, and there was no evidence of a dose-relationship to frequency of adverse events. The results therefore support the conduct of clinical trials to investigate efficacy, tolerability and pharmacokinetics during repeated dosing.
Intramolecular Cycloadditions between Cyclobutadiene and Alkenes (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTIntramolecular Cycloadditions between Cyclobutadiene and AlkenesJohn A. Tallarico, Michele L. Randall, and Marc L. SnapperView Author Information Eugene F. Merkert Chemistry Center, Boston College Chestnut Hill, Massachusetts 02167-3860 Cite this: J. Am. Chem. Soc. 1996, 118, 38, 9196–9197Publication Date (Web):September 25, 1996Publication History Received16 April 1996Published online25 September 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja9612559https://doi.org/10.1021/ja9612559rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views982Altmetric-Citations48LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Addition reactions,Cyclization,Functionalization,Hydrocarbons,Oxidation Get e-Alerts
Effects of cortisone with and without heparin on angiogenesis induced by prostaglandin e1 and by s180 cells, and on growth of murine transplantable tumours (1985)

Cortisone acetate, locally applied in sustained-release pellets, is effective in inhibiting angiogenesis induced by prostaglandin E1 in the rabbit cornea. The inhibitory effect of cortisone is not increased by addition of heparin. Similar results were obtained with angiogenesis induced by S180 cells. The effects of cortisone with and without heparin were also studied on 5 transplantable murine tumours: 3 variants of B16 melanoma, Lewis lung carcinoma and fibrosarcoma M4. The effect of cortisone in slowing the growth rate of tumours was modestly potentiated by heparin, but no regression of the tumour mass occurred.
Discontinuous DNA Replication (1980)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Cytokine and growth factor production by monocytes/macrophages on protein preadsorbed polymers (1992)

These studies evaluate the effect of biomedical polymers: Biomer, polydimethyl-siloxane (PDMS), polyethylene, expanded polytetrafluoroethylene (ePTFE), Dacron, and the control polystyrene with or without adsorbed proteins IgG, fibrinogen, and fibronectin on the ability of activated human monocytes/macrophages to produce Interleukin 1 Beta (IL-1-B), Interleukin 6 (IL-6), and Tumor Necrosis Factor Alpha (TNF-A). Monocytes/macrophages incubated on biomedical polymers with or without protein preadsorption produce variable levels of IL-1-B, IL-6, and TNF-A dependent on the polymer and adsorbed protein. IL-6 was produced in the greatest quantity and was the most influenced by protein adsorption. ePTFE and PDMS polymers were least stimulating while polystyrene was the most stimulating of monocyte activity. Adsorbed IgG consistently altered the ability of the polymers to activate monocytes/macrophages to produce cytokines. These studies provide important insight into conditions which modulate monocyte/macrophage activity in response to protein preadsorbed biomedical polymers.
Evaluation of the conformational free energies of loops in proteins (1994)

In this paper we discuss the problem of including solvation free energies in evaluating the relative stabilities of loops in proteins. A conformational search based on a gas-phase potential function is used to generate a large number of trial conformations. As has been found previously, the energy minimization step in this process tends to pack charged and polar side chains against the protein surface, resulting in conformations which are unstable in the aqueous phase. Various solvation models can easily identify such structures. In order to provide a more severe test of solvation models, gas-phase conformations were generated in which side chains were kept extended so as to maximize their interaction with the solvent. The free energies of these conformations were compared to that calculated for the crystal structure in three loops of the protein E. coli RNase H, with lengths of 7, 8, and 9 residues. Free energies were evaluated with a finite difference Poisson-Boltzmann (FDPB) calculation for electrostatics and a surface area-based term for nonpolar contributions. These were added to a gas-phase potential function. A free energy function based on atomic solvation parameters was also tested. Both functions were quite successful in selecting, based on a free energy criterion, conformations quite close to the crystal structure for two of the three loops. For one loop, which is involved in crystal contacts, conformations that are quite different from the crystal structure were also selected. A method to avoid precision problems associated with using the FDPB method to evaluate conformational free energies in proteins is described.
No facilitator required for membrane transport of hydrogen sulfide (2009)

Hydrogen sulfide (H(2)S) has emerged as a new and important member in the group of gaseous signaling molecules. However, the molecular transport mechanism has not yet been identified. Because of structural similarities with H(2)O, it was hypothesized that aquaporins may facilitate H(2)S transport across cell membranes. We tested this hypothesis by reconstituting the archeal aquaporin AfAQP from sulfide reducing bacteria Archaeoglobus fulgidus into planar membranes and by monitoring the resulting facilitation of osmotic water flow and H(2)S flux. To measure H(2)O and H(2)S fluxes, respectively, sodium ion dilution and buffer acidification by proton release (H(2)S left arrow over right arrow H(+) + HS(-)) were recorded in the immediate membrane vicinity. Both sodium ion concentration and pH were measured by scanning ion-selective microelectrodes. A lower limit of lipid bilayer permeability to H(2)S, P(M,H(2)S) >or = 0.5 +/- 0.4 cm/s was calculated by numerically solving the complete system of differential reaction diffusion equations and fitting the theoretical pH distribution to experimental pH profiles. Even though reconstitution of AfAQP significantly increased water permeability through planar lipid bilayers, P(M,H(2)S) remained unchanged. These results indicate that lipid membranes may well act as a barrier to water transport although they do not oppose a significant resistance to H(2)S diffusion. The fact that cholesterol and sphingomyelin reconstitution did not turn these membranes into an H(2)S barrier indicates that H(2)S transport through epithelial barriers, endothelial barriers, and membrane rafts also occurs by simple diffusion and does not require facilitation by membrane channels.
Fluorocarbon Nitrogen Compounds. III.<sup>1</sup> Some Reactions of Bis-(trifluoromethyl)-amine, (CF<sub>3</sub>)<sub>2</sub>NH<sup>2</sup> (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluorocarbon Nitrogen Compounds. III.1 Some Reactions of Bis-(trifluoromethyl)-amine, (CF3)2NH2John A. Young, Skevos N. Tsoukalas, and Richard D. DresdnerCite this: J. Am. Chem. Soc. 1958, 80, 14, 3604–3606Publication Date (Print):July 1, 1958Publication History Published online1 May 2002Published inissue 1 July 1958https://doi.org/10.1021/ja01547a030RIGHTS & PERMISSIONSArticle Views231Altmetric-Citations44LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (395 KB) Get e-Alerts Get e-Alerts
Fast detection of cells using a continuously scalable Mexican-hat-like template (2010)

We propose a fast algorithm for the detection of cells in fluorescence images. The algorithm, which estimates the number of cells and their respective centers and radii, relies on the fast computation of intensity-based correlations between the cells and a near-isotropic Mexican-hat-like detector. The attractive features of our algorithm are its speed and accuracy. The former attribute is derived from the fact that we can compute correlations between a cell and detectors of various sizes using O(1) operations; whereas, it is our ability to continuously control the center and the radius of the detector that results in a precise estimate of the position and size of the cell. We provide experimental results on both simulated and real data to demonstrate the speed and accuracy of the algorithm.
Catalytic C−H Insertions Using Iron(III) Porphyrin Complexes (2008)

Fe(III), Cu(II), and Ag(II) porphyrin complexes are active catalysts for benzylic and ring C−H insertions by carbene fragments transferred from methyl diazomalonate, 2. Temperatures above 100 °C are required, and yields greater than 70% have been achieved. C−H insertions with cyclohexane and tetrahydrofuran are catalyzed at a lower temperature of 60 °C with 60% yields when para-substituted methyl 2-phenyldiazoacetates, 15a−d, are used as carbene sources. The rate for Fe(TPP)Cl-catalyzed insertion into the C−H bond of cyclohexane was found to be first-order in the concentration of methyl 2-(p-chlorophenyl)diazoacetate, p-Cl-MPDA, indicating that formation of a carbene complex is the rate-determining step. Competition reactions for cyclohexane insertion with para-substituted methyl 2-phenyldiazoacetates correlated linearly with σ+ Hammett parameters with a ρ value of –1.11 ± 0.05 when Fe(TPP)Cl was used as a catalyst, demonstrating that electron-donating para-substituents on the phenyl group of the methyl 2-aryldiazoacetates enhanced reactivity. These data are consistent with the involvement of an electrophilic iron−carbene complex in the catalytic cycle. A mechanistic model for the iron-mediated C−H insertion reactions is proposed.
ABSTRACT: Entrapment of Petroleum under Hydrodynamic Conditions (1952)

ABSTRACT Despite its effectiveness as a basis for petroleum exploration, the anticlinal theory represents but a special case of oil and gas accumulation and is valid only when the associated ground water is in hydrostatic equilibrium. Since ground water need not be at rest, a more general formulation valid for both hydrostatic and hydrodynamic conditions is required. Oil and gas possess energy with respect to their positions and environment, which when referred to unit mass may be termed the potential at any given point of the fluid considered. When the potential of a specified fluid in a region of underground space is not constant an unbalanced force will act upon the fluid tending to drive it in the direction in which its potential decreases. Hence oil and gas in a dispersed state underground tend to migrate from regions of higher to those of lower energy levels, and come ultimately to rest in positions which constitute traps, where their potentials assume locally minimum or least values. Most often traps for petroleum are regions of low potential which are enclosed jointly by regions of higher potential and impermeable barriers. End_Page 2-------------------------- Oil and gas migration occurs through a normally water-saturated environment. If the water is at rest, oil and gas equipotential surfaces will be horizontal, the impelling forces will be directed vertically upward, and the traps will be the familiar ones of the anticlinal theory. If the water is in motion in a nonvertical direction, the oil and gas equipotentials will be tilted downward in the flow direction with those for oil inclined at a greater angle than those for gas. The impelling forces for oil and for gas will not be parallel and the two fluids will migrate in divergent directions to traps which will not in general coincide and may, in fact, be separated entirely, a trap for oil being incapable of holding gas, and vice versa. Under hydrodynamic conditions accumulations of oil or gas will invariably exhibit inclined oil- or gas-water interfaces with the angle of inclination given by tan = [dz]/[dx] = [w]/[w-o] [dh]/[dx] , where dz/dx is the slope of the interface, w the density of the water and o that of the oil (or gas), and dh/dx the component of the hydraulic gradient of the water in the direction x. Stable oil and gas accumulations may be found in anticlines but they may equally well occur in structural terraces, noses, monoclines, and other unclosed structures entirely devoid of lithologic barriers to updip migration. End_Page 3-------------------------- Not only are these effects theoretically expectable, but they occur, with tilts ranging from tens to hundreds of feet per mile, in almost every major oil-producing area. If many such accumulations are not to be overlooked, we are faced with the necessity of supplementing our customary knowledge of structure and stratigraphy with the three-dimensional ground-water hydrology of every petroliferous basin. End_of_Record - Last_Page 4---------
Geometry and kinematics of dog ribs (1989)

Five anesthetized supine beagle dogs were scanned using a fast, multislice computed tomographic X-ray technique to determine the orientation of the ribs at total lung capacity (TLC) and functional residual capacity (FRC). A plane was fit to each rib using a coordinate system in which the z-axis was aligned approximately cephalocaudally and the x-z-plane coincided with the sagittal midplane. The orientation of each plane was described by "pump-handle" and "bucket-handle" angles. The ribs rotated downward and inward during a passive deflation of the lungs from TLC to FRC. Rib displacement was not uniform: bucket-handle motion was predominant in the upper ribs, and pump- and bucket-handle motions were equal in the lower ribs. The change in the pump-handle angles between TLC and FRC was approximately 6 degrees for ribs 3-8, and the change in the bucket-handle angles decreased with rib number from 16 degrees for rib 3 to 6 degrees for rib 8. Rib shape was described by fitting an ellipse to the data for each rib; the ribs became larger and more circular with increasing rib number.
Investigating the effects of fine-grain three-dimensional integration on microarchitecture design (2008)

In this article we propose techniques that enable efficient exploration of the 3D design space, where each logical block can span more than one silicon layer. Fine-grain 3D integration provides reduced intrablock wire delay as well as improved power consumption. However, the corresponding power and performance advantage is usually underutilized, since various implementations of multilayer blocks require novel physical design and microarchitecture infrastructure to explore 3D microarchitecture design space. We develop a cubic packing engine which can simultaneously optimize physical and architectural design for efficient vertical integration. This technique selects the individual unit designs from a set of single-layer or multilayer implementations to get the best microarchitectural design in terms of performance, temperature, or both. Our experimental results using a design driver of a high-performance superscalar processor show a 36% performance improvement over traditional 2D for 2--4 layers and 14% over 3D with single-layer unit implementations. Since thermal characteristics of 3D integrated circuits are among the main challenges, thermal-aware floorplanning and thermal via insertion techniques are employed to keep the peak temperatures below threshold.
Understanding and Exploiting Design-Induced Latency Variation in Modern DRAM Chips (2016)

Variation has been shown to exist across the cells within a modern DRAM chip. We empirically demonstrate a new form of variation that exists within a real DRAM chip, induced by the design and placement of different components in the DRAM chip. Our goals are to understand design-induced variation that exists in real, state-of-the-art DRAM chips, exploit it to develop low-cost mechanisms that can dynamically find and use the lowest latency at which to operate a DRAM chip reliably, and, thus, improve overall system performance while ensuring reliable system operation. To this end, we first experimentally demonstrate and analyze designed-induced variation in modern DRAM devices by testing and characterizing 96 DIMMs (768 DRAM chips). Our characterization identifies DRAM regions that are vulnerable to errors, if operated at lower latency, and finds consistency in their locations across a given DRAM chip generation, due to design-induced variation. Based on our extensive experimental analysis, we develop two mechanisms that reliably reduce DRAM latency. First, DIVA Profiling uses runtime profiling to dynamically identify the lowest DRAM latency that does not introduce failures. DIVA Profiling exploits design-induced variation and periodically profiles only the vulnerable regions to determine the lowest DRAM latency at low cost. Our second mechanism, DIVA Shuffling, shuffles data such that values stored in vulnerable regions are mapped to multiple error-correcting code (ECC) codewords. Combined together, our two mechanisms reduce read/write latency by 40.0%/60.5%, which translates to an overall system performance improvement of 14.7%/13.7%/13.8% (in 2-/4-/8-core systems) across a variety of workloads, while ensuring reliable operation.
Covalent Joining of Phenylalanine Transfer Ribonucleic Acid Half-Molecules by T4 RNA Ligase (1974)

RNA ligase from T4-phage-infected Escherichia coli cells catalyzes the covalent joining of two polynucleotides that are partially hydrogen-bonded to each other. Two polynucleotide fragments derived from yeast tRNA(Phe) and consisting of residues 1-36 and 38-74 are covalently joined by the enzyme. The product of the reaction lacks residue Y(37) and has an anticodon loop with six nucleotide residues, whereas all tRNA species whose sequences have so far been determined have seven nucleotides in this loop. Evidence is also presented for the formation of a polynucleotide-adenylylate intermediate in the joining reaction, in which a pyrophosphate bond links the 5'-phosphoryl terminus of the polynucleotide and the phosphoryl group of AMP.
Characteristics of the Berkeley multicusp ion source (1979)

The performance of a cubical permanent magnet generated line-cusp ion source has been investigated for use with neutral beam injectors. This source has been operated with discharge currents greater than 500 A and ion current densities higher than 400 mA/cm2 at the extraction grid. The uniformity of the density profile across the extraction area is found to be dependent on the gas pressure. By using a fast Langmuir probe sweeping circuit, the electron temperature and the plasma density and potential have been analyzed for different discharge powers and gas pressures. The heat load on the plasma grid when it is electrically floating or connected to the negative cathode has been compared calorimetrically. The use of lanthanum hexaboride and impregnated oxide cathodes have been investigated for the purpose of long pulse operation. The phenomenon of mode flipping is found to occur quite frequently during a discharge with these magnetic-field-free cathodes. Species composition as a function of discharge power and chamber length is measured by a mass spectrometer.
The Relation of Virologic and Immunologic Markers to Clinical Outcomes after Nucleoside Therapy in HIV-Infected Adults with 200 to 500 CD4 Cells per Cubic Millimeter (1996)

Both the risk of the progression of HIV disease and the efficacy of antiretroviral therapy are strongly associated with the plasma level of HIV RNA and with the viral phenotype. The changes in the plasma concentration of HIV RNA predict the changes in CD4 cell counts and survival after treatment with reverse-transcriptase inhibitors.