gebhart/patrepeval huggingface dataset:
Mechanism of GTP hydrolysis by p21N-ras catalyzed by GAP: Studies with a fluorescent GTP analog (1993)

The mechanism of the hydrolysis of GTP by p21N-ras and its activation by the catalytic domain of p120 GTPase activating protein (GAP) have been studied using a combination of chemical and fluorescence measurements with the fluorescent GTP analogue, 2'(3')-O-(N-methylanthraniloyl)GTP (mantGTP). Since the concentration of active p21 is important in these measurements, various assays for both total protein and active p21 were investigated. All assays gave good agreement except the filter binding assay of [3H]-GDP bound to p21, which gave values of 35-40% compared to the other methods. Concentrations of p21 were thus based on the absorbance of the mant-chromophore of the p21-mant-nucleotide complexes. The rate constants of the elementary steps of the p21 intrinsic GTPase activity and the GAP activated activity were similar between GTP and mantGTP. Incubation of a stoichiometric complex of p21.mantGTP results in a biphasic decrease in fluorescence. The second phase occurs with the same rate constant as the cleavage step and is accelerated by GAP. No other steps of the mechanism are affected by GAP. Incubation of a stoichiometric complex of p21.mantGpp[NH]p also results in a biphasic decrease in fluorescence even though cleavage does not occur. This is interpreted that the cleavage step of p21.GTP is preceded by and controlled by an isomerization of the p21.GTP complex. GAP accelerates the rate constant of the second fluorescence phase occurring with p21.mantGpp[NH]p. This result shows that GAP accelerates the proposed isomerization which limits GTP cleavage rather than the cleavage step itself.
Altered surface tension of lung extracts and lung mechanics (1965)

Reduction of the surface area of 24 extracts of rabbit lungs by four-fifths decreased the surface tension to a minimum value of 0–5 dynes/cm at 18–22 C. However, minimum surface tension was above 15 dynes/cm if 1) the temperature was raised to 42 C, 2) the extract was prepared with distilled water, 3) phospholipase C was incubated with the extract, and 4) cholesterol or oleic acid was added to the surface. If blood or serum was added during the extraction, minimum surface tension was usually (although not invariably) elevated. Rinsing diluted rat serum or chylomicrons through the airways increases elastic recoil of excised rat lungs. Other reports show that heating a lung above 42 C or rinsing a solution of phospholipase C through the airways also increases elastic recoil of excised rat lungs. Therefore, these conditions alter the surface tension of lung extracts and the pressure-volume characteristics of the lungs concordantly. In addition, we found that the surface tension of lung extracts was not stable below 24 dynes/cm. Similar instability of the surface within the lung should lead to gradual atelectasis if a low transpulmonary pressure is maintained. elastic recoil; atelectasis; compliance; lung surface Submitted on January 21, 1965
MANAGEMENT OF INFECTION AT THE SITE OF A TOTAL KNEE ARTHROPLASTY (2005)

Infection following total knee arthroplasty remains a major complication in joint reconstruction, resulting in significant morbidity to the patient and increased hospital costs. The diagnosis of infection is often made based on clinical criteria, although adjunctive measures including blood work, plain radiographs, and arthrocentesis are often helpful in confirming the diagnosis and planning subsequent treatment. For patients in whom the diagnosis of infection cannot be immediately confirmed, an acute intraoperative tissue analysis by a skilled pathologist and experienced surgeon is required. Treatment of this complication is directed by the chronicity of the infection, stability of the components, and medical status of the patient. Although débridement with component retention may be successful in the acute postoperative stage of joint replacement, a two-staged revision with removal of all components followed by an adequate course of parenteral antibiotics prior to reimplantation remains the gold standard for eradicating chronic infection. The addition of antibiotic-impregnated cement spacers (static or articulating) has also been implicated as a useful adjunct to treatment. Long-term suppressive antibiotic treatment, arthrodesis, resection arthroplasty, and amputation are reserved for specific clinical situations in which a staged revision or débridement are unlikely to yield favorable results.
3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography (2015)

Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1-3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.
Vascular Endothelial Growth Factor (VEGF) Expression in Human Coronary Atherosclerotic Lesions (1998)

These results demonstrate distinct expression of VEGF and its receptors (flt-1 and Flk-1) in atherosclerotic lesions in human coronary arteries. Considering the multipotent actions of VEGF documented experimentally in vivo and in vitro, our findings suggest that VEGF may have some role in the progression of human coronary atherosclerosis, as well as in recanalization processes in obstructive coronary diseases.
Pre-Adipocyte Proliferation and Differentiation in Response to Hormone Supplementation of Decapitated Fetal Pig Sera (1987)

Growth hormone and thyroid hormones have been implicated as important serum factors for adipocyte development in cell culture. Fetal decapitation removes these factors from serum of the growing fetal pig and results in development of fewer adipocytes than in intact fetuses. These experiments examined the effects of growth hormone or thyroxine supplementation to decapitated fetal pig sera upon pre-adipocyte proliferation and differentiation. Hormones were supplemented to concentrations present in sera from intact pig littermates (reference). Sera +/- hormones were analyzed for their effects upon pre-adipocyte proliferation as determined by [3H]-thymidine incorporation; enzyme expression as determined by sn-glycerol-3-phosphate dehydrogenase activity; and induction of complete differentiation into lipid filled adipocytes as based upon a pre-adipocyte proliferation and enzyme expression than reference sera. Growth hormone had no effect in decap sera upon these parameters. Decap sera permitted detection of 54% more lipid-accumulating, newly formed adipocytes on percol gradients than reference sera, but growth hormone reduced detection to 29% of reference sera. Thyroxine specifically stimulated pre-adipocyte proliferation more than decap sera, but not to the level of reference sera. Complete differentiation, a formation of lipid-accumulating adipocytes was promoted also by thyroxine in comparison to basal decap sera. The results of these experiments indicate thyroid hormones are an important component of fetal sera for regulation of adipocyte development, whereas growth hormone may only affect cellular metabolism and not promote pre-adipocyte growth and development.
Low-k interconnect stack with multi-layer air gap and tri-metal-insulator-metal capacitors for 14nm high volume manufacturing (2015)

We describe here Intel's 14nm high-performance logic technology interconnects and back end stack featuring 13 metal layers and a tri-metal laminated metal-insulator-metal (MIM) capacitor. For the first time on a logic product in high volume, multiple layers (M4 and M6) incorporate an air gap integration scheme to deliver up to 17% RC benefit. Pitch Division patterning is introduced to deliver high yield capable interconnect layers with a minimum pitch of 52nm.
Preclinical Results Supporting Therapeutic Development of Mrg-106, an Oligonucleotide Inhibitor of Mir-155, in CTCL (2015)

Abstract Treatment-resistant hematological malignancies remain an area of high unmet need and novel therapeutic approaches will be required. microRNAs are small (~ 22 nt) non-coding RNAs that act as negative regulators of gene expression. These small RNAs impact expression of a substantial fraction of the genome, and have powerful effects on cellular phenotypes and physiological processes. miR-155-5p is a well-described oncomiR associated with poor prognosis in multiple malignancies, particularly lymphoma and leukemia. Cutaneous T-cell lymphoma (CTCL) is a rare hematological malignancy with limited treatment options and a strong mechanistic link to increased miR-155-5p. Because of the accessibility of cutaneous lesions, CTCL provides a unique opportunity to determine if inhibition of miR-155-5p has therapeutic potential in lymphomas associated with elevated miR-155-5p. We optimized a LNA-modified oligonucleotide inhibitor of miR-155-5p, MRG-106, based on the ability to de-repress canonical miR-155-5p targets in multiple cell types in vitro. In mycosis fungoides (MF) cell lines, MRG-106 does not require additional formulation to achieve maximum pharmacodynamic efficacy. Inhibition of miR-155-5p resulted in transcriptome changes consistent with miR-155-5p target gene modulation, reduction in cell proliferation, and activation of the programmed cell death pathway. The gene expression and phenotypic effects were inhibitor dose-dependent and sequence-specific. Based on an informatics approach for the expression profiling of MF cell lines treated with MRG-106, a set of 600 genes was identified to represent the translational pharmacodynamic biomarker signature, both direct and downstream of miR-155-5p. GLP preclinical safety studies have been completed in rats and non-human primates, demonstrating an acceptable safety profile for MRG-106. We plan to initiate a 4-week first-in-human clinical trial in CTCL (MF) patients. The trial design is two-part, with Part A testing the effect of direct intra-tumoral injection of MRG-106 into plaque and nodular skin lesions, and Part B testing the effect of systemic (subcutaneous) administration of higher doses of MRG-106. The primary objective of Part A is to profile the pharmacodynamic effect of MRG-106 on the miR-155-5p gene expression signature, establishing a PK/PD model to guide future development. The primary objective of Part B is to establish the safety, tolerability, PK and skin deposition of MRG-106 after systemic delivery. Exploratory objectives include measures for clinical response, immune system effects, and biomarker validation. Disclosures Seto: miRagen Therapeutics: Employment, Equity Ownership. Beatty:miRagen Therapeutics: Employment, Equity Ownership. Pestano:miRagen Therapeutics: Employment, Equity Ownership. Dickinson:miRagen Therapeutics: Employment, Equity Ownership. Warren:miRagen Therapeutics: Consultancy. Rodman:miRagen Therapeutics: Employment, Equity Ownership. Jackson:miRagen Therapeutics: Employment, Equity Ownership.
Humanized Anti-Trop-2 IgG-SN-38 Conjugate for Effective Treatment of Diverse Epithelial Cancers: Preclinical Studies in Human Cancer Xenograft Models and Monkeys (2011)

The anti-Trop-2 hRS7-CL2A-SN-38 ADC provides significant and specific antitumor effects against a range of human solid tumor types. It is well tolerated in monkeys, with tissue Trop-2 expression similar to humans, at clinically relevant doses, and warrants clinical investigation.
Lipid Bilayers at Gel/Gel Interface for Ion Channel Recordings (2008)

We have developed a practical method to produce durable artificial lipid bilayers using a hydrogel-hydrogel interface for ion channel measurements. Bilayers were formed by forcing a hydrogel-bead into contact with the hydrogel layer (hydrogel plate) in a lipid solution. The immediate formation of a bilayer was observed (<1 s). This allows channel recordings to be repeated more easily and quickly as compared to conventional methods. Currents of various types of channel such as gramicidin, hemolysin and BK-channel have been recorded. Our channel property results mirrored those of other techniques and were reproducible. Hydrogel solutions containing gramicidin were extremely stable and could be used months after preparation for bilayer experiments. [DOI: 10.1380/ejssnt.2008.130]
Formation and Bleaching Properties of the T Bands in KCl (1966)

Optical bleaching of additively colored or 60Co irradiated KCl with ``F light'' and/or red light at 100°C produces three new absorption bands at 839 mμ (T1), 894 mμ (T2), and 992 mμ (T3) which have been designated as ``T bands.'' The most prominent T band is T2, with a thermal stability exceeding the R and N bands and less than the M and F bands. Illumination of a crystal containing T bands at −195°C causes a temporary interconversion between the T2 and T3 bands, the direction depending on the spectral intensity of the ambient light. The transformation kinetics were investigated with 20-μsec pulse and steady bleaching techniques and were found to be of first order. The rate constants are linear functions of the light absorption rates in the T2 and T3 bands with significant dark contributions. The analysis indicates that the temporarily bleached T2 and T3 centers maintain a constant concentration ratio. The available information indicates that the T bands are due to distinct F-aggregate color centers, possibly isomers of F5, and that the T2 and T3 centers are closely related in structure.
Introduction of histidine residues into avidin subunit interfaces allows pH‐dependent regulation of quaternary structure and biotin binding (2003)

In order to turn the subunit association and biotin binding of avidin into pH-sensitive phenomena, we have replaced individually three amino acid residues in avidin (Met96, Val115 and Ile117) with histidines in the 1-3 interface, and in combination with a histidine conversion in the 1-2 interface (Trp110). The single replacements Met96His and Val115His in the 1-3 interface were found to have a clear effect on the quaternary structure of avidin, since subunit associations of these mutants became pH-dependent. The histidine replacement in the 1-2 interface affected the biotin-binding properties of the mutants, in particular reversibility of binding and protein-ligand complex formation were pH-sensitive, as measured by IAsys biosensor and fluorescence correlation spectroscopy, respectively. The possibility of regulating the quaternary structure and function of avidin in a controlled and predictable manner, due to introduced interface histidines, will expand even further the range and versatility of the avidin-biotin technology.
Enantioselective addition of organozinc reagents to aldehydes (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantioselective addition of organozinc reagents to aldehydesKenso Soai and Seiji NiwaCite this: Chem. Rev. 1992, 92, 5, 833–856Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/cr00013a004https://doi.org/10.1021/cr00013a004research-articleACS PublicationsRequest reuse permissionsArticle Views5280Altmetric-Citations1172LEARN 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-Alertsclose Get e-Alerts
WSN01-1: Frame Aggregation and Optimal Frame Size Adaptation for IEEE 802.11n WLANs (2006)

The IEEE 802.11a/b/g have been widely accepted as the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">de</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">facto</i> standards for wireless local area networks (WLANs). The recent IEEE 802.11n proposals aim at providing a physical layer transmission rate of up to 600 Mbps. However, to fully utilize this high data rate, the current IEEE 802.11 medium access control (MAC) needs to be enhanced. In this paper, we investigate the performance improvement of the MAC protocol by using the two frame aggregation techniques, namely A-MPDU (MAC Protocol Data Unit Aggregation) and A-MSDU (MAC Service Data Unit Aggregation). We first propose an analytical model to study the performance under uni-directional and bi-directional data transfer. Our proposed model incorporates packet loss either from collisions or channel errors. Comparison with simulation results show that the model is accurate in predicting the network throughput. We also propose an optimal frame size adaptation algorithm with A-MSDU under error-prone channels. Simulation results show that the network throughput performance is significant improved when compared with both randomized and fixed frame aggregation algorithms.
An iterative approach to the beam hardening correction in cone beam CT (2000)

In computed tomography (CT), the beam hardening effect has been known to be one of the major sources of deterministic error that leads to inaccuracy and artifact in the reconstructed images. Because of the polychromatic nature of the x-ray source used in CT and the energy-dependent attenuation of most materials, Beer's law no longer holds. As a result, errors are present in the acquired line integrals or measurements of the attenuation coefficients of the scanned object. In the past, many studies have been conducted to combat image artifacts induced by beam hardening. In this paper, we present an iterative beam hardening correction approach for cone beam CT. An algorithm that utilizes a tilted parallel beam geometry is developed and subsequently employed to estimate the projection error and obtain an error estimation image, which is then subtracted from the initial reconstruction. A theoretical analysis is performed to investigate the accuracy of our methods. Phantom and animal experiments are conducted to demonstrate the effectiveness of our approach.
Biosynthesis of the Escherichia coli K4 Capsule Polysaccharide (1997)

Escherichia coli K4 bacteria synthesize a capsule polysaccharide (GalNAc-GlcA(fructose))n with the carbohydrate backbone identical to chondroitin. GlcA- and GalNAc-transferase activities from the bacterial membrane were assayed with acceptors derived from the capsule polysaccharide and radiolabeled UDP-[14C]GlcA and UDP-[3H]GalNAc, respectively. It was shown that defructosylated oligosaccharides (chondroitin) could serve as substrates for both the GlcA- and the GalNAc-transferases. The radiolabeled products were completely degraded with chondroitinase AC; the [14C]GlcA unit could be removed by beta-D-glucuronidase, and the [3H]GalNAc could be removed by beta-N-acetylhexosaminidase. A fructosylated oligosaccharide acceptor tested for GlcA-transferase activity was found to be inactive. These results indicate that the chain elongation reaction of the K4 polysaccharide proceeds in the same way as the polymerization of the chondroitin chain, by the addition of the monosaccharide units one by one to the nonreducing end of the polymer. This makes the biosynthesis of the K4 polysaccharide an interesting parallel system for studies of chondroitin sulfate biosynthesis. In the biosynthesis of capsule polysaccharides from E. coli, a similar mechanism has earlier been demonstrated for polysialic acid (NeuNAc)n (Rohr, T. E., and Troy, F. A. (1980) J. Biol. Chem. 255, 2332-2342) and for the K5 polysaccharide (GlcAbeta1-4GlcNAcalpha1-4)n (Lidholt, K., Fjelstad, M., Jann, K., and Lindahl, U. (1994) Carbohydr. Res. 255, 87-101). In contrast, chain elongation of hyaluronan (GlcAbeta1-3GlcNAcbeta1-4)n is claimed to occur at the reducing end (Prehm, P. (1983) Biochem. J. 211, 181-189).
Function and regulation of the cyanobacterial genes lexA, recA and ruvB: LexA is critical to the survival of cells facing inorganic carbon starvation (2004)

The cyanobacterial genes lexA, recA and ruvB were analysed in Synechocystis PCC6803, which is shown here to be more radiation resistant than the other unicellular model strain Synechococcus PCC7942. We found that cyanobacteria do not have an Escherichia coli-type SOS regulon. The Synechocystis lexA and recA promoters were found to be strong and UV insensitive, unlike the ruvB promoter, which is weak and UV-C inducible. Yet, lexA and recA are regulated by UV-C, but the control is negative and occurs at the post-transcriptional level. Two novel conserved elements were characterized in the lexA promoter: (i) an unusually long crucial box 5'-TAAAATTTTGTATCTTTT-3' (-64, -47); and (ii) a negatively acting motif 5'-TAT GAT-3' (-42, -37). These elements were not found in the recA promoter, which appeared to be unusually simple in harbouring only a single crucial element (i.e. the canonical -10 box). RuvB, operating in recombination-dependent cellular processes, was found to be dispensable to cell growth, whereas LexA and RecA appeared to be critical to cell viability. Using DNA microarrays, we have identified 57 genes with expression that is altered, at least twofold, in response to LexA depletion. None of these genes is predicted to operate in DNA metabolism, arguing against the involvement of LexA in the regulation of DNA repair. Instead, most of the LexA-responsive genes were known to be involved in carbon assimilation or controlled by carbon availability. Consistently, the growth of the LexA-depleted strain was found to be strongly dependent on the availability of inorganic carbon.
Waveguide-Integrated Si Nano-Photodiode with Surface-Plasmon Antenna and its Application to On-chip Optical Clock Distribution (2008)

We developed a waveguide-integrated Si nano-photodiode (PD) with a surface plasmon (SP) antenna for on-chip optical clock distribution. The interfacial periodic nano-scale metal–semiconductor–metal Schottky electrodes were shown to function as an SP optical antenna and also as an optical coupler between a SiON waveguide and a very thin Si-absorption layer. Furthermore, a very high speed response of 17 ps as well as enhanced photoresponsivity was achieved for a 10-µm coupling length. By using this technology, we fabricated a prototype of a large-scale-integration (LSI) on-chip optical clock system and demonstrated 5 GHz of optical clock circuit operation connected with a 4-branching H-tree structure.