gebhart/patrepeval huggingface dataset:
Nucleic Acid-Dependent Cross-Linking of the Nucleocapsid Protein of Sindbis Virus (2000)

The assembly of the alphavirus nucleocapsid core is a multistep event requiring the association of the nucleocapsid protein with nucleic acid and the subsequent oligomerization of capsid proteins into an assembled core particle. Although the mechanism of assembly has been investigated extensively both in vivo and in vitro, no intermediates in the core assembly pathway have been identified. Through the use of both truncated and mutant Sindbis virus nucleocapsid proteins and a variety of cross-linking reagents, a possible nucleic acid-protein assembly intermediate has been detected. The cross-linked species, a covalent dimer, has been detected only in the presence of nucleic acid and with capsid proteins capable of binding nucleic acid. Optimum nucleic acid-dependent cross-linking was seen at a protein-to-nucleic-acid ratio identical to that required for maximum binding of the capsid protein to nucleic acid. Identical results were observed when cross-linking in vitro assembled core particles of both Sindbis and Ross River viruses. Purified cross-linked dimers of truncated proteins and of mutant proteins that failed to assemble were found to incorporate into assembled core particles when present as minor components in assembly reactions, suggesting that the cross-linking traps an authentic intermediate in nucleocapsid core assembly. Endoproteinase Lys-C mapping of the position of the cross-link indicated that lysine 250 of one capsid protein was cross-linked to lysine 250 of an adjacent capsid protein. Examination of the position of the cross-link in relation to the existing model of the nucleocapsid core suggests that the cross-linked species is a cross-capsomere contact between a pentamer and hexamer at the quasi-threefold axis or is a cross-capsomere contact between hexamers at the threefold axis of the icosahedral core particle and suggests several possible assembly models involving a nucleic acid-bound dimer of capsid protein as an early step in the assembly pathway.
Diabetes Exacerbates Inflammatory Responses to Ischemia-Reperfusion (1996)

These results indicate that diabetes mellitus is associated with exaggerated leukocyte-endothelial cell adhesion and albumin leakage responses to ischemia-reperfusion. The enhanced leukocyte accumulation in response to ischemia-reperfusion is mediated by CD11/CD18-ICAM-1 interactions (firm adhesion) and P-selectin (rolling). The exaggerated albumin leakage response to ischemia-reperfusion in diabetics is not mediated by the recruited inflammatory cells.
Phosphonate Ester Probes for Proteolytic Antibodies (2001)

The reactivity of phosphonate ester probes with several available proteolytic antibody (Ab) fragments was characterized. Irreversible, active site-directed inhibition of the peptidase activity was evident. Stable phosphonate diester-Ab adducts were resolved by column chromatography and denaturing electrophoresis. Biotinylated phosphonate esters were applied for chemical capture of phage particles displaying Fv and light chain repertoires. Selected Ab fragments displayed enriched catalytic activity inhibitable by the selection reagent. Somewhat unexpectedly, a phosphonate monoester also formed stable adducts with the Abs. Improved catalytic activity of phage Abs selected by monoester binding was evident. Turnover values (kcat) for a selected Fv construct and a light chain against their preferred model peptide substrates were 0.5 and 0.2 min(-1), respectively, and the corresponding Michaelis-Menten constants (Km) were 10 and 8 microm. The covalent reactivity of Abs with phosphonate esters suggests their ability to recapitulate the catalytic mechanism utilized by classical serine proteases.
Analysis of the recognition mechanism of the alternative pathway of complement by monoclonal anti‐factor H antibodies: evidence for multiple interactions between H and surface bound C3b (1996)

The ability of the alternative pathway of complement to discriminate targets as either activators or non-activators is mediated by different binding properties of factor H to surface-associated C3b molecules. In the present study we have probed the interaction between H and C3b using five anti-H mAb. The binding sites of the mAb were mapped by Western blotting using both recombinant and trypsin-generated H fragments. Two mAb bound to CCP1 (90X, 196X), two to CCP5 (MRC OX24, 86X) and one to CCP8-15a (131X). At a molar ratio 2:1 of 125I-H:mAb all tested mAb enhanced binding of H to both activator- and non-activator-bound C3b. At higher concentrations two mAb had an inhibitory effect on H binding to surface-associated C3b (OX24, 131X). Thus the mAb 131X inhibits H binding to surface-bound C3b but unlike OX24 it does not bind to the previously described C3b binding site within or near CCP4-5. These results indicate that there is an additional interaction site on factor H for surface-bound C3b.
Fluorescence lifetime quenching studies on the accessibilities of actin sulfhydryl sites (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFluorescence lifetime quenching studies on the accessibilities of actin sulfhydryl sitesTerence Tao and Joan ChoCite this: Biochemistry 1979, 18, 13, 2759–2765Publication Date (Print):June 26, 1979Publication History Published online1 May 2002Published inissue 26 June 1979https://pubs.acs.org/doi/10.1021/bi00580a011https://doi.org/10.1021/bi00580a011research-articleACS PublicationsRequest reuse permissionsArticle Views186Altmetric-Citations52LEARN 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
Identification of the Apoptosis Activation Cascade Induced in Mammary Carcinomas by Energy Restriction (2004)

Energy restriction (ER) inhibits mammary carcinogenesis and results in a marked reduction in tumor size, effects likely to be explained by ER-mediated induction of apoptosis. The goal of this study was to investigate the molecular mechanism(s) accounting for apoptosis induction. To do this, chemically induced mammary carcinomas were evaluated from rats that were ad libitum fed (control), 40% ER, or 40% ER but energy repleted for 7 days before study termination (ER-REP); the ER-REP group permitted the determination of the reversibility of ER-mediated effects. Cleaved products of poly(ADP-ribose) polymerase 1 were elevated by ER (P < 0.025) providing biochemical evidence of apoptosis induction. cDNA microarray analysis identified the Bcl-2, CARD, and IAP functional gene groupings as being involved in apoptosis induction. Consistent with the microarray data, the activities of caspases 9 and 3 were observed to be approximately 2-fold higher in carcinomas from ER rats (P < or =0.01), whereas caspase 8 activity was similar in carcinomas from all three of the groups. This evidence that ER-induced apoptosis mediated by the mitochondrial pathway was additionally supported by the finding that levels of Bcl-2, Bcl-xl, and XIAP protein were significantly lower (P < 0.01), and levels of Bax and Apaf-1 were elevated (P < 0.02) in ER carcinomas versus those carcinomas from control or ER-REP rats. Additional studies revealed that Akt phosphorylation (activation) was reduced in mammary carcinomas from ER rats. Thus, it appears that ER induces apoptosis in mammary carcinomas via a cell survival factor-dependent pathway.
THE BACTERIOLOGY OF ACNE (1972)

Journal Article THE BACTERIOLOGY OF ACNE Get access J. A. SAVIN J. A. SAVIN Skin Department, St Thomas Hospital, London, S.E.1 Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, Volume 86, Issue s8, 1 June 1972, Pages 3–9, https://doi.org/10.1111/j.1365-2133.1972.tb15407.x Published: 01 June 1972
RESULTS OF TREATMENT OF PATIENTS WITH HYPERTENSION BY TOTAL THORACIC AND PARTIAL TO TOTAL LUMBAR SYMPATHECTOMY, SPLANCHNICECTOMY AND CELIAC GANGLIONECTOMY (1949)

Grimson, Keith S. M.D.; Orgain, Edward S. M.D.; Anderson, Banks M.D.; Broome, Robert A. Jr. M.D.; Longino, Frank H. M.D. Author Information
GaAs/AlGaAs electro-optic modulator with bandwidth> 40 GHz (1995)

A high speed GaAs/AlGaAs travelling wave Mach-Zehnder electro-optic modulator has been fabricated. The device uses a novel slow wave electrode design to achieve phase velocity matching and has a measured electrical bandwidth &gt; 40 GHz.
A prostate cancer vaccine comprising whole cells secreting IL-7, effective against subcutaneous challenge, requires local GM-CSF for intra-prostatic efficacy (2008)

A panel of cytokine-secreting RM-9 prostate cancer cells were tested as whole cell vaccines to determine their capacity to evoke an anti-prostate cancer immune response. In our model, vaccines secreting mGM-CSF or mIL-7 resulted in the highest increase in circulating T lymphocytes after vaccination, prolonged survival and, in a proportion of animals, tumor-free survival. Anti-tumor effects were more evident after a subcutaneous RM-9 challenge than after an intraprostatic challenge. However, when the RM-9/mGM-CSF cell line was used as intraprostatic tumor challenge, protection after RM-9/mIL-7 vaccination was restored.
The distribution and radiation effects of intravenously administered colloidal Au198 in man (1954)

LINEALLY, radioactive colloidal gold has C been administered interstitially, into cavities, and intravenously. T h e distribution and effect are greatly influenced by the route of administration. T h e present report is entirely concerned with the intravenous injection of this material.
Conditional variable importance for random forests (2008)

The resulting conditional variable importance reflects the true impact of each predictor variable more reliably than the original marginal approach.
Antenna-on-Chip and Antenna-in-Package Solutions to Highly Integrated Millimeter-Wave Devices for Wireless Communications (2009)

Antenna-on-chip (AoC) and antenna-in-package (AiP) solutions are studied for highly integrated millimeter-wave (mmWave) devices in wireless communications. First, the background, regulations, standard, and applications of 60-GHz wireless communications are briefly introduced. Then, highly integrated 60-GHz radios are overviewed as a basis for the link budget analysis to derive the antenna gain requirement. Next, in order to have deep physical insight into the AoC solution, the silicon substrate's high permittivity and low resistivity effects on the AoC efficiency are examined. It is shown that the AoC solution has low efficiency, less than 12% due to large ohmic losses and surface waves, which requires the development of techniques to improve the AoC efficiency. After that, the AiP solution and associated challenges such as how to realize low-loss interconnection between the chip and antenna are addressed. It is shown that wire-bonding interconnects, although inferior to the flip-chip, are still feasible in the 60-GHz band if proper compensation schemes are utilized. An example of the AiP solution in a low-temperature cofired ceramic (LTCC) process is presented in the 60-GHz band showing an efficiency better than 90%. A major concern with both AoC and AiP solutions is electromagnetic interference (EMI), which is also discussed. Finally, the systems level pros and cons of both AoC and AiP solutions are highlighted from the electrical and economic perspectives for system designers.
Comparative Ribosomal Protein Sequence Analyses of a Phylogenetically Defined Genus, Pseudomonas, and Its Relatives (1995)

I analyzed various families of ribosomal proteins obtained from selected species belonging to the genus Pseudomonas sensu stricto and allied organisms which were previously classified in the genus Pseudomonas. Partial amino acid sequencing of L30 preparations revealed that the strains which I examined could be divided into three clusters. The first cluster, which was assigned to the genus Pseudomonas sensu stricto, included Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas mendocina, and Pseudomonas fluorescens. The second cluster included Burkholderia pickettii and Burkholderia plantarii. The third cluster, which was a deeply branching cluster in the stem of gram-negative bacteria, included Brevundimonas diminuta and Brevundimonas vesicularis. Despite the different levels of conservation of the N-terminal sequences of ribosomal protein families (the highest level of similarity was 74% for L27 proteins and the lowest level of similarity was 42% for L30 proteins), similar phylogenetic trees were constructed by using data obtained from sequence analyses of various ribosomal protein families, including the S20, S21, L27, L29, L31, L32, and L33 protein families. Thus, I demonstrated the efficacy of ribosomal protein analysis in bacterial taxonomy.
Hijacking the translation apparatus by RNA viruses (2002)

As invading viruses do not harbor functional ribosomes in their virions, successful amplification of the viral genomes requires that viral mRNAs compete with cellular mRNAs for the host cell translation apparatus. Several RNA viruses have evolved remarkable strategies to recruit the host translation initiation factors required for the first steps in translation initiation by host cell mRNAs. This review describes the ways that three families of RNA viruses effectively usurp limiting translation initiation factors from the host.
Generation of 5-fluorouracil from 5-fluorocytosine by monoclonal antibody-cytosine deaminase conjugates (1991)

Cytosine deaminase (CDase) catalyzes the conversion of cytosine to uracil and is also able to convert the clinically used antifungal agent 5-fluorocytosine (5FC) into the anticancer drug 5-fluorouracil (5FU). The enzyme was purified from bakers' yeast in a six-step procedure. Studies indicated that bakers' yeast CDase had a molecular weight of approximately 32 kDa and was composed of two subunits of equal molecular weights. Monoclonal antibodies were covalently attached to CDase, forming conjugates that could bind to antigens on tumor cell surfaces. The combination of L6-CDase and 5FC was equivalent in cytotoxic activity to 5FU when tested against the H2981 human lung adenocarcinoma cell line (L6 positive, 1F5 negative). 5FC alone was noncytotoxic. The activation of 5FC was immunologically specific since 1F5-CDase did not enhance 5FC activity.
Corticospinal excitability accompanying ballistic wrist movements in primary dystonia (2004)

Current models of basal ganglia dysfunction in primary dystonia propose that the excessive muscle activity results from an increase in the excitability of the primary motor cortex. Neurophysiological and neuroimaging studies, however, have shown consistently reduced movement-related sensorimotor cortical activity. To explore this paradox, we used transcranial magnetic stimulation (TMS) to examine changes in corticospinal excitability preceding and during ballistic movements of the wrist in 9 patients with primary dystonia affecting the arm and 9 matched control subjects. The onset time, rate of rise, and duration of changes in the excitability of corticospinal projections to the agonist muscle were normal in the patients with dystonia. Increases in excitability were selective to the initial agonist muscle, suggesting that the spatial recruitment of corticospinal neurons was normal. Nonetheless, movements were slower in the patients by an average of 26%. The onset of the first agonist muscle burst was normal in magnitude and timing but the activity in this muscle subsequently became attenuated as movement progressed. Muscle activity in antagonist and proximal muscles of the upper arm was reduced significantly in the dystonia patients. These findings support the view that movement preparation and initiation at the level of the primary motor cortex is normal in patients with dystonia. Bradykinesia could not be attributed to co-contraction or overflow of activity and was associated with reduced rather than excessive muscle activity.
Extended-spectrum β-lactamases in Enterobacteriaceae isolated in Brazil carry distinct types of plasmid-mediated quinolone resistance genes (2013)

One hundred and six nalidixic acid-resistant Enterobacteriaceae isolates from two Brazilian hospitals isolated from June to October 2010 were evaluated to characterize the co-existence of plasmid-mediated quinolone resistant (PMQR) and extended-spectrum β-lactamase (ESBL) determinants. The qnr genetic environment was determined by PCR and sequencing. Conjugation and hybridization experiments determined whether qnr-carrying plasmids were self-transferable. The aac(6')-Ib-cr and qepA genes were also screened. Thirteen qnr-like genes (12.3 %) were identified, with qnrB1 the most common, followed by qnrS1, qnrB2 and qnrB19. No qnrA, qnrC, qnrD or qepA determinant was detected. All qnr-positive strains possessed chromosomal substitutions in gyrase- and topoisomerase-encoding genes and four harboured a aac(6')-Ib-cr gene. The co-production of blaCTX-M was observed in ten qnr-positive strains. These results indicate the dissemination of PMQR genes shown in clinical isolates from Brazil, and their co-existence with ESBL genes emphasizes the complexity of plasmid-mediated resistance determinants among Enterobacteriaceae.
Ultra-pH-Sensitive Nanoprobe Library with Broad pH Tunability and Fluorescence Emissions (2014)

pH is an important physiological parameter that plays a critical role in cellular and tissue homeostasis. Conventional small molecular pH sensors (e.g., fluorescein, Lysosensor) are limited by broad pH response and restricted fluorescent emissions. Previously, we reported the development of ultra-pH-sensitive (UPS) nanoprobes with sharp pH response using fluorophores with small Stokes shifts (<40 nm). In this study, we expand the UPS design to a library of nanoprobes with operator-predetermined pH transitions and wide fluorescent emissions (400-820 nm). A copolymer strategy was employed to fine tune the hydrophobicity of the ionizable hydrophobic block, which led to a desired transition pH based on standard curves. Interestingly, matching the hydrophobicity of the monomers was critical to achieve a sharp pH transition. To overcome the fluorophore limitations, we introduced copolymers conjugated with fluorescence quenchers (FQs). In the micelle state, the FQs effectively suppressed the emission of fluorophores regardless of their Stokes shifts and further increased the fluorescence activation ratios. As a proof of concept, we generated a library of 10 nanoprobes each encoded with a unique fluorophore. The nanoprobes cover the entire physiologic range of pH (4-7.4) with 0.3 pH increments. Each nanoprobe maintained a sharp pH transition (on/off < 0.25 pH) and high fluorescence activation ratio (>50-fold between on and off states). The UPS library provides a useful toolkit to study pH regulation in many pathophysiological indications (e.g., cancer, lysosome catabolism) as well as establishing tumor-activatable systems for cancer imaging and drug delivery.
Spectral cues used in the localization of sound sources on the median plane (1974)

The spectral cues used for median-plane localization are described by three experiments. First, the frequency spectrum necessary for localization is measured by noting the accuracy of subjects localizing low- and high-pass-filtered white noise. Second, several high-pass, low-pass, bandpass, and bandstop filters are associated with the subjective impression of direction by observing what directions are most frequently perceived by subjects localizing white noise colored by each filter. Third, the frequency responses of several artificial ears are measured for different angles of median-plane sound incidence. Results show that sound spectra from 4 to 16 kHz are necessary for localization. Frontal cues are a 1-octave notch, with a lower-frequency cutoff between 4 and 10 kHz and increased energy above 13 kHz. The “above” cue is a 1/4-octave peak between 7 and 9 kHz, with a high-frequency cutoff at 10 kHz. The “behind” cue is a small peak from 10 to 12 kHz. Increases in frontal elevation are signaled by an increase in the lower cutoff frequency of the 1-octave notch. This notch appears to be generated by time-delayed reflections off the posterior concha wall interfering with sound directly entering the external auditory canal.
The implementation of POSTGRES (1990)

The design and implementation decisions made for the three-dimensional data manager POSTGRES are discussed. Attention is restricted to the DBMS backend functions. The POSTGRES data model and query language, the rules system, the storage system, the POSTGRES implementation and the current status and performance are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Study of optically induced degradation of conductivity in hydrogenated amorphous silicon by transient grating method (1983)

Optically induced degradation of the conductivity (the Staebler–Wronski effect) in glow discharge hydrogenated amorphous Si was examined by a transient grating method. It was clarified that the Staebler–Wronski effect was a bulk and not a surface effect, and the origin of the decrease of the photoconductivity was mainly attributed to the decrease of the lifetime instead of the mobility.
Diamond family of nanoparticle superlattices (2016)

Diamond lattices formed by atomic or colloidal elements exhibit remarkable functional properties. However, building such structures via self-assembly has proven to be challenging because of the low packing fraction, sensitivity to bond orientation, and local heterogeneity. We report a strategy for creating a diamond superlattice of nano-objects via self-assembly and demonstrate its experimental realization by assembling two variant diamond lattices, one with and one without atomic analogs. Our approach relies on the association between anisotropic particles with well-defined tetravalent binding topology and isotropic particles. The constrained packing of triangular binding footprints of truncated tetrahedra on a sphere defines a unique three-dimensional lattice. Hence, the diamond self-assembly problem is solved via its mapping onto two-dimensional triangular packing on the surface of isotropic spherical particles.
Novel Applications of Polymerase Chain Reaction to Urinary Nucleic Acid Analysis (2006)

DNA fragments from cells that have died throughout the body not only appear in the bloodstream but also cross the kidney barrier into the urine. The relatively low molecular weight (150-200 bp) of this Transrenal DNA should be considered when deciding on methods of isolation and analysis. In particular, if polymerase chain reaction (PCR) is used for amplification and detection of specific sequences, then the reduction of amplicon size will significantly enhance sensitivity. Detection of DNA mutations is also made more difficult by the presence of a large excess of a wild-type allele. Using K-RAS mutations as an example, two ways around this problem--enriched PCR and stencil-aided mutation analysis-are described, based on selective pre-PCR elimination of wild-type sequences.