gebhart/patrepeval huggingface dataset:
Biological and immunological properties of human immunodeficiency virus type 1 envelope glycoprotein: analysis of proteins with truncations and deletions expressed by recombinant vaccinia viruses (1991)

The effects of C-terminal and internal deletions on the synthesis, transport, biological properties, and antigenicity of the human immunodeficiency virus type 1 envelope protein were determined. A family of recombinant vaccinia viruses that express N-terminal overlapping env proteins of 204, 287, 393, 502 (full-length gp120), 635, 747, and 851 (full-length gp160) amino acids was constructed. All of the proteins were detected in intra- and extracellular forms which differed in the extent of glycosylation. The 747- and 851-amino-acid proteins were cleaved, were expressed on the surface of infected cells, and bound CD4. The 635-amino-acid env protein was cleaved inefficiently, and both the precursor and product were secreted, indicating absence of the transmembrane sequence. The 635- as well as the 502-amino-acid protein, which was also largely secreted, could still bind CD4. Unexpectedly, the 393-amino-acid protein was anchored in the plasma membrane, but neither it nor smaller proteins bound to soluble CD4. When amino acids at the gp120-gp41 junction were deleted, proteolytic cleavage of gp160 did not occur. Nevertheless, gp160 was inserted into the plasma membrane and bound soluble CD4. The predominant conserved B-cell epitopes were mapped to gp41 and the C terminus of gp120, whereas cytotoxic T-cell epitopes were distributed throughout the length of the glycoproteins.
Reduction in Halothane Anesthetic Requirement by Clonidine, an Alpha-Adrenergic Agonist (1982)

The effects of clonidine, a potent central alpha-adrenergic agonist, and of tolazoline, an alpha-adrenergic antagonist, on the minimal anesthetic concentration (MAC) of halothane were studied in male mongrel dogs. Control halothane MAC was 0.8 +/- 0.04 vol% (determined in each dog by gas chromatography of arterial blood, n = 30). Clonidine, 5 microgram/kg (n = 10) and 20 microgram/kg (n = 10), give slowly intravenously, maximally reduced MAC by 42% (at 2.3 hours after clonidine) and 48% (at 2.6 hours after clonidine) for each dose. In another set of animals (n = 5) an alpha-adrenergic antagonist, tolazoline, 5 mg/kg IV, reversed the clonidine-induced reduction in halothane MAC rapidly and completely. Tolazoline alone, 5 mg/kg, (n = 5) had no significant effect on halothane MAC. Thus, the administration of the central alpha-adrenergic agonist clonidine decreased the required anesthetic concentration of halothane, as defined by MAC, by almost half. This effect, as it is reversed by tolazoline, is likely to be mediated through a central alpha-adrenergic receptor mechanism.
Prolonged survival of B-lineage acute lymphoblastic leukemia cells is accompanied by overexpression of bcl-2 protein (1993)

Overexpression of bcl-2 delays the onset of apoptosis in lymphohematopoietic cells. We measured levels of bcl-2 protein in normal and leukemic human B-cell progenitors with a specific monoclonal antibody and flow cytometry. Normal immature B cells had low levels of bcl-2 protein; the intensity of fluorescence, expressed as molecules of soluble fluorochrome per cell, within CD10+ cells was 3,460 +/- 1,050 (mean +/- SD; 5 samples). In 16 cases of B-lineage acute lymphoblastic leukemia (ALL), cells had levels of bcl-2 that were strikingly higher than those of their normal counterparts (33,560 +/- 14,570; P < .001 by t-test analysis). We next investigated whether the intensity of bcl-2 expression correlated with the resistance of immature B cells to in vitro culture. In 12 cases of B-lineage ALL, the cells recovered after 7 days of culture on allogeneic bone marrow stromal layers were 69% to 178% (median, 95.5%) of those originally seeded. Prolonged survival of leukemic cells in vitro was observed even in the absence of stromal layers in 6 of these 12 cases; the intensity of bcl-2 protein expression in these cases was 45,000 +/- 13,270, compared with 21,500 +/- 7,260 in the 6 cases in which greater than 99.5% of cells rapidly died by apoptosis under the same culture conditions (P = .003). Five immature B-cell lines, continuously growing in the absence of stroma, had the highest bcl-2 expression (79,400 +/- 20,330). By contrast, most normal CD19+, sIg-immature B cells died despite the presence of bone marrow stromal layers; 9.7% to 28.2% were recovered after 7 days of culture in three experiments. We conclude that abnormal bcl-2 gene expression influences the survival ability of B-cell progenitors. This may contribute to leukemogenesis and explain the aptitude of leukemic lymphoblasts to expand outside the bone marrow microenvironment.
Characterization of the Degradation Products of a Color-Changed Monoclonal Antibody: Tryptophan-Derived Chromophores (2014)

We describe the characterization of degradation products responsible for color change in near UV-visible light-irradiated and heat-stressed monoclonal antibody (mAb) drug product in liquid formulation. The treated samples were characterized using reversed-phase HPLC and size-exclusion HPLC with absorption spectroscopy. Both methods showed color change was due to chromophores formed on the mAb but not associated with the formulation excipients in both light-irradiated and heat-stressed mAb samples. These chromophores were further located by a new peptide mapping methodology with a combination of mass spectrometry and absorption spectroscopy. Mass spectrometry identified the major tryptophan oxidation products as kynurenine (Kyn), N-formylkynurenine (NFK), and hydroxytryptophan (OH-Trp). The absorption spectra showed that each of the tryptophan oxidation products exhibited a distinct absorption band above 280 nm shifted to the longer wavelengths in the order of OH-Trp < NFK < Kyn. The Kyn-containing peptide was detected by absorption at 420 nm. No new absorption bands were observed for either methionine or histidine oxidation products. This confirmed that tryptophan oxidation products, but not methionine and histidine oxidation products, were responsible for the color change. It is worth noting that a new oxidation product with the loss of hydrogen (2 Da mass decrease) for Trp-107 of the heavy chain was identified in the heat-stressed mAb sample. This oxidized tryptophan residue exhibited a distinct absorption band at the maximum absorbance wavelength 335 nm, which is responsible for the color change to yellow. This study showed that the new peptide mapping methodology with a combination of mass spectrometry and absorption spectroscopy is useful to identify tryptophan oxidation products as chromophores responsible for color change in stressed mAb drug product.
Nitro reduction as an electronic switch for bioreductive drug activation. (1997)

It is well known that the reduction of aromatic nitro groups can give rise to toxic species, and that net nitro reduction by one-electron reductases can usually be inhibited by oxygen. There has been much interest in utilizing this biotransformation to activate drugs in hypoxic regions of tumors, but no clinically useful compound has yet resulted. Nitroreductive activation of prodrugs by oxygen-insensitive (and oxygen-sensitive) reductases is also of current interest because of new methods for introducing specific nitroreductases into tumors (e.g., as antibody-enzyme conjugates or by gene therapy). In most of the compounds investigated previously, cytotoxicity appears to be due to reactive nitroso or hydroxylamine reduction products arising from the nitro group itself. It is argued that there is greater scope for designing potent and selective nitro compounds by using the nitro group as an electronic switch to activate a latent reactive moiety elsewhere in the molecule. Examples of this approach include the nitro(hetero)aromatic mustards (e.g., SN 23816, NSC 646394) in which the nitro group controls the reactivity of a nitrogen mustard to which it is directly conjugated, and the nitro(hetero)aromatic methylquaternary (NMQ) mustards (e.g., SN 25341, NSC 658926) in which reduction of the nitro group triggers fragmentation of the molecule to release a reactive aliphatic nitrogen mustard. Many of these compounds show very high selectivity for hypoxic cells in culture. Some are also active against hypoxic cells in tumors, and provide large tumor growth delays when combined with tumor blood flow inhibitors such as 5,6-dimethylxanthenone-4-acetic acid (DMXAA). These prodrug designs also have potential for releasing effectors other than nitrogen mustards, which opens up many possibilities for use of nitro compounds as tumor-selective prodrugs.
Stress confinement, shock wave formation, and laser-induced damage (2005)

The concept of confinement is that if energy deposition into a system occurs during durations shorter than a confinement time, the response of the system depends only on the total energy deposited and not on the deposition time. For stress confinement, the relevant response is the pressure that is produced. We have shown previously that for laser absorption by a spherical absorber, stress confinement is not valid at the core of the absorber and the tensile stresses continue to grow as the pulse duration shrinks well below any characteristic response time of the system. We have now calculated the pressure response in the cellular medium outside the absorber. We find that for a variety of energies, stress confinement is valid. We find that the characteristic confinement time agrees well with that expected for pressure transmission across the absorber. We show that even though the peak pressure that is produced varies slowly as a function of pulse duration, there is a sudden onset of shock wave production when the pulse duration is shortened below the confinement time. Since damage results from pressure gradients, the sudden onset of shock waves implies a sharp increase in the potential for damage.
Generalized gradient approximation for the exchange-correlation hole of a many-electron system (1996)

We construct a generalized gradient approximation (GGA) for the density ${\mathit{n}}_{\mathrm{xc}}$(r,r+u) at position r+u of the exchange-correlation hole surrounding an electron at r, or more precisely for its system and spherical average 〈${\mathit{n}}_{\mathrm{xc}}$(u)〉=(4\ensuremath{\pi}${)}^{\mathrm{\ensuremath{-}}1}$\ensuremath{\int}d${\mathrm{\ensuremath{\Omega}}}_{\mathit{u}}$ ${\mathit{N}}^{\mathrm{\ensuremath{-}}1}$\ensuremath{\int}${\mathit{d}}^{3}$r n(r)${\mathit{n}}_{\mathrm{xc}}$(r,r+u). Starting from the second-order density gradient expansion, which involves the local spin densities ${\mathit{n}}_{\mathrm{\ensuremath{\uparrow}}}$(r),${\mathit{n}}_{\mathrm{\ensuremath{\downarrow}}}$(r) and their gradients \ensuremath{\nabla}${\mathit{n}}_{\mathrm{\ensuremath{\uparrow}}}$(r),\ensuremath{\nabla}${\mathit{n}}_{\mathrm{\ensuremath{\downarrow}}}$(r), we cut off the spurious large-u contributions to restore those exact conditions on the hole that the local spin density (LSD) approximation respects. Our GGA hole recovers the Perdew-Wang 1991 and Perdew-Burke-Ernzerhof GGA's for the exchange-correlation energy, which therefore respect the same powerful hole constraints as LSD. When applied to real systems, our hole model provides a more detailed test of these energy functionals, and also predicts the observable electron-electron structure factor. \textcopyright{} 1996 The American Physical Society.
Synthesis of imenine. Route to 4-oxygenated oxoaporphines (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of imenine. Route to 4-oxygenated oxoaporphinesM. P. Cava and I. NoguchiCite this: J. Org. Chem. 1973, 38, 1, 60–62Publication Date (Print):January 1, 1973Publication History Published online1 May 2002Published inissue 1 January 1973https://doi.org/10.1021/jo00941a010Request reuse permissions Article Views56Altmetric-Citations22LEARN 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 (414 KB) Get e-Alertsclose Get e-Alerts
Construction of a general vector for efficient expression of mammalian proteins in bacteria: use of a synthetic ribosome binding site. (1981)

With the premise that mRNAs transcribed in Escherichia coli from cloned eukaryotic DNA inserts do not possess the necessary regulatory signals for recognition by prokaryotic ribosomes, we have constructed a general plasmid vector carrying a chemically synthesized prokaryotic ribosome binding site that will ensure the efficient expression of eukaryotic proteins in E. coli. In addition to the regulatory signals necessary for ribosome recognition, the synthetic segment contains, at one end, a Pst I cleavage site which will direct its insertion to pBR322 DNA and, at the other end, a HindIII site to facilitate attachment of the passenger eukaryotic gene. Using simian virus 40 (SV40) tumor (t) antigen as a model system, we have ligated the SV40 DNA fragment containing the entire t antigen gene in tandem with the synthetic ribosome binding site to pBR322 DNA at the Pst I site, which lies within the coding sequence of the beta-lactamase gene. Initiation of transcription at the beta-lactamase promoter would produce a chimeric mRNA with the synthetic ribosome binding signals and the SV40 sequence flanked by beta-lactamase coding sequences. Utilization of the synthetic regulatory signals for initiation of translation is demonstrated by the efficient synthesis, in bacterial transformants, of authentic SV40 t antigen. Excision of the entire SV40 insert by HindIII from those clones that have retained intact HindIII sites at the junction between the ribosome binding site and the SV40 sequence would allow insertion of other heterologous DNAs by using HindIII linkers. The efficient expression of any DNA insert would require that the entire coding sequence be contiguous and that its termini be randomized by treatment with exonuclease III and nuclease S1 to vary the distance between the translational initiation codon and the synthetic ribosome binding site.
Fine-tuning of T-cell receptor avidity to increase HIV epitope variant recognition by cytotoxic T lymphocytes (2010)

These results indicate that rationally targeted increases in functional avidities can be utilized to maximize the antiviral breadth of transgenic TCRs. In contrast to previously reported random mutagenesis to markedly increase functional avidities, tuning through recombining naturally occurring polymorphisms may offer a more physiologic approach that minimizes the risk of deleterious TCR reactivities.
Synthesis and structure of a complex of bismuth(III) with a nitrogen donor macrocycle (1995)

The synthesis and structure of the first example of a bismuth(III) complex of a nitrogen donor macrocycle is reported, with the pendant-donor cyclen-based tetraaza macrocycle 1,4,7,10-tetrakis[(S)-2-hydroxypropyl]-1,4,7,10-tetraazacyclo-dodecane; the complex is eight-coordinate with approximately square antiprismatic coordination geometry.
ANTIVIRAL ACTIVITY OF TENOFOVIR (PMPA) AGAINST NUCLEOSIDE-RESISTANT CLINICAL HIV SAMPLES (2001)

The presence of the lamivudine-associated M184V RT mutation increases tenofovir susceptibility in multiple HIV genotypes. Tenofovir is uniquely active against multinucleoside-resistant HIV expressing the Q151M mutation, but shows reduced susceptibility to the T69S insertion mutations. HIV with common forms of zidovudine and lamivudine resistance are susceptible to tenofovir, corroborating phase II clinical results demonstrating the activity of tenofovir DF in treatment-experienced patients.
On the Survival of Frozen Bacteria (1961)

SUMMARY: Steadily growing Aerobacter aerogenes organisms were largely killed by slow freezing in buffer or by freeze drying. 100% survival was obtained after dropping bacteria suspended in 10% aqueous glycerol into liquid nitrogen and thawing. Ten per cent solutions of diethylene glycol, i-erythritol, glucose, sucrose or polyethylene glycol (MW = 10,000) protected equally well; the last three substances did not penetrate the cell cytoplasm. The most lethal medium was dilute NaCl; broth, water or a dilute salt mixture were moderately lethal. These findings are incompatible with the view that the lethal effects of freezing are connected with osmotic shock or that protection from freezing damage requires (a) penetration of the protective agent or (b) osmotic dehydration of the cytoplasm. Cells frozen and thawed, even with a protective agent, showed a lowered rate of glycerol oxidation and a higher death rate when starved at the optimal temperature and pH value for growth. The storage life of frozen organisms at −20° depended on the protective agent used; only glycerol permitted extended storage.
β-galactosidase Determination by an Electrochemical Biosensor Mediated with Ferrocene (2011)

Abstract: In this paper, a new viewpoint on the activity determination of β-galactosidase is reported. Glucose oxidase was directly immobilized on a glassy carbon electrode and mediated by ferrocene. The biosensor's performance was based on mediated electron transfer by ferrocene, which reduced via glucose oxidase reaction. In this reaction, substrate of glucose oxidase, glucose was provided by the activity of β-galactosidase in the sample. The parameters of the fabrication process for the electrode were optimized. Experimental conditions influencing the biosensor performance, such as pH, ferrocene and lactose concentrations, and temperature, were investigated and assessed. Finally, the biosensor was successfully applied to determination of β-galactosidase activity of artificial intestinal juice.
Diffusion tensor imaging: Concepts and applications (2001)

The success of diffusion magnetic resonance imaging (MRI) is deeply rooted in the powerful concept that during their random, diffusion-driven displacements molecules probe tissue structure at a microscopic scale well beyond the usual image resolution. As diffusion is truly a three-dimensional process, molecular mobility in tissues may be anisotropic, as in brain white matter. With diffusion tensor imaging (DTI), diffusion anisotropy effects can be fully extracted, characterized, and exploited, providing even more exquisite details on tissue microstructure. The most advanced application is certainly that of fiber tracking in the brain, which, in combination with functional MRI, might open a window on the important issue of connectivity. DTI has also been used to demonstrate subtle abnormalities in a variety of diseases (including stroke, multiple sclerosis, dyslexia, and schizophrenia) and is currently becoming part of many routine clinical protocols. The aim of this article is to review the concepts behind DTI and to present potential applications.
Recombinant Activated Factor VII (rFVIIa): Characterization, Manufacturing, and Clinical Development (2001)

Recombinant activated coagulation factor VII (rFVIIa) (NovoSeven) was developed for treatment of bleeding in hemophilia patients with inhibitors (antibodies) against factors VIII or IX. rFVIIa initiates the coagulation cascade by binding to tissue factor at the site of injury and causes the formation of sufficient amounts of thrombin to trigger coagulation. Patients with a variety of other coagulation deficiencies than hemophilia characterized by an impaired thrombin generation and life-threatening bleeding have been reported as successfully treated with rFVIIa. Data are now entered into clinical registries established to further monitor this experimental treatment with NovoSeven. rFVIIa is produced free of any added human protein. The amino acid sequence of rFVIIa is identical to plasma-derived FVIIa (pdFVIIa). Posttranslational modifications (i.e., gamma-carboxylations, N- and O-glycosylations) are qualitatively identical in pdFVIIa and rFVIIa although some quantitative differences exist. The activities of rFVIIa and pdFVIIa are indistinguishable. Manufacturing of rFVIIa involves expression in baby hamster kidney (BHK) cells followed by purification, including three ion-exchange and one immunoaffinity chromatography steps. The last anion-exchange chromatography step ensures completion of the autoactivation of recombinant factor VII (rFVII) to rFVIIa. This review describes the mechanism of action, characterization, manufacturing, and preclinical and current clinical evidence for the efficacy and safety of rFVIIa.
Inhibition of ALK5 Signaling Induces Physeal Dysplasia in Rats (2007)

TGF-beta, and its type 1 (ALK5) receptor, are critical to the pathogenesis of fibrosis. In toxicologic studies of 4 or more days in 10-week-old Sprague-Dawley rats, using an ALK5 inhibitor (GW788388), expansion of hypertrophic and proliferation zones of femoral physes were noted. Subphyseal hyperostosis, chondrocyte hypertrophy/hyperplasia, and increased matrix were present. Physeal zones were laser microdissected from ALK5 inhibitor-treated and control rats sacrificed after 3 days of treatment. Transcripts for TGF-beta1, TGF-beta2, ALK5, IHH, VEGF, BMP-7, IGF-1, bFGF, and PTHrP were amplified by real-time PCR. IGF and IHH increased in all physis zones with treatment, but were most prominent in prehypertrophic zones. TGF-beta2, bFGF and BMP7 expression increased in proliferative, pre-and hypertrophic zones. PTHrP expression was elevated in proliferative zones but decreased in hypertrophic zones. VEGF expression was increased after treatment in pre- and hypertrophic zones. ALK5 expression was elevated in prehypertrophic zones. Zymography demonstrated gelatinolytic activity was reduced after treatment. Apoptotic markers (TUNEL and caspase-3) were decreased in hypertrophic zones. Proliferation assessed by Topoisomerase II and Ki67 was increased in multiple zones. Movat stains demonstrated that proteoglycan deposition was altered. Physeal changes occurred at doses well above those resulting in fibrosis. Interactions of factors is important in producing the physeal dysplasia phenotype.
Clinical Information Technologies and Inpatient Outcomes (2009)

Hospitals with automated notes and records, order entry, and clinical decision support had fewer complications, lower mortality rates, and lower costs.