gebhart/patrepeval huggingface dataset:
Reversible conformational changes and fusion activity of rabies virus glycoprotein (1991)

In an attempt to understand the implication of the rabies virus glycoprotein (G) in the first steps of the viral cycle, we studied the pH dependence of virus-induced fusion and hemagglutination, as well as modifications of the structure and properties of the viral glycoprotein following pH acidification. Our results suggest that the G protein adopts at least three distinct configurations, each associated with different properties. At neutral pH, G did not fuse membranes or hemagglutinate erythrocytes. It was insensitive to digestion with bromelain and trypsin. At pH 6.4, the glycoprotein became sensitive to proteases. Hemagglutination was at its maximum and then sharply decreased with the pH. No fusion was detected. Aggregation of virus was also observed. The third configuration, at below pH 6.1, was associated with the appearance of fusion. Some neutralizing monoclonal antibodies were able to differentiate these three configurations. Preincubation of the virus at below pH 6 inhibited fusion, but this inhibition, like the structural modifications of the glycoprotein, was reversible when G was reincubated at neutral pH.
Evidence for [2 + 2] and [4 + 2] cycloadditions of allylic Grignard reagents to benzyne (1977)

J. Duboudin, B. Jousseaume and M. Pinet, J. Chem. Soc., Chem. Commun., 1977, 454 DOI: 10.1039/C39770000454
Reduction of parasitic bipolar transistor actionand punchthrough susceptibilityin MOSFETs using Si/Si 1-x Ge x sources and drains (1996)

Silicon CMOS devices are subject to some limitations as the dimensions are scaled down for VLSI applications. The incorporation of SiGe into the p-channel device can reduce parasitic bipoiar action and punchthrough susceptibility. The authors compare the properties of elevated source and drain devices with and without Si1-xGex in the source and drain regions. We show that the parasitic bipolar gain is reduced by a factor of 18 and that the punchthrough effects seen in silicon devices are absent in the Si0.8Ge0.2 devices.
Surface acoustic wave microsensors and applications (1997)

Surface acoustic wave (SAW) devices have been studied for the last twenty years as highly sensitive yet relatively inexpensive microsensors for applications ranging from temperature and stress to gas and biological sensing. This wide range of applications is due to the SAW microsensors' high sensitivity to several physical parameters including mass, temperature, stress, and conductivity. Their low cost results from the use of standard batch microelectronic fabrication techniques for their manufacture. In this paper several chemical sensing applications for SAW devices are described. These include: gas detection; thin-film polymer characterization; dew-point measurements; surface energy measurements; and as a method to measure surface cleanliness. Experimental results are presented along with comparisons to other measurement techniques.
Hypervariable region peptides variably induce specific anti-idiotypic antibodies: an approach to determining antigenic dominance. (1986)

Rats and rabbits were immunized with synthetic peptides corresponding to the VH hypervariable regions of several alpha (1----3) dextran-specific antibodies from mice to study the efficacy of synthetic peptides in the generation of site-specific anti-idiotypic reagents. Synthetic peptides were made which corresponded to the HV1, HV2, and HV3 hypervariable regions of the heavy chain of M104 (IdX+, IdI-(M104)+), HV2 of HDex 14 (IdX-), and HV3 of J558 (IdX+, IdI(J558)+). The HV1(M104) peptide sequence is found in all dextran-specific immunoglobulins examined and the HV2 and the HV3 peptides span the regions implicated in IdX and IdI expression, respectively. Sera from many rabbits and rats indicate that all five peptides are immunogenic. Antisera to HV3 peptides show excellent binding to the appropriate myeloma proteins, with antisera to the HV3(M104) peptide demonstrating little binding to proteins that differ in HV3 sequence. Antisera generated against HV1(M104) and both HV2 peptides show weak cross-reaction to the appropriate proteins; however, these sera are not idiotypic because they cross-react with immunoglobulins with very limited sequence homology. Thus, it appears that some, but not all synthetic peptides from hypervariable regions will be capable of generating antisera with useful anti-idiotypic specificities. This may reflect differences in the intrinsic antigenicity of various parts of the VH region.
Effect of Convalescent Plasma Therapy on Time to Clinical Improvement in Patients With Severe and Life-threatening COVID-19 (2020)

Chinese Clinical Trial Registry: ChiCTR2000029757.
Anticancer potential of curcumin: preclinical and clinical studies. (2003)

Curcumin (diferuloylmethane) is a polyphenol derived from the plant Curcuma longa, commonly called turmeric. Extensive research over the last 50 years has indicated this polyphenol can both prevent and treat cancer. The anticancer potential of curcumin stems from its ability to suppress proliferation of a wide variety of tumor cells, down-regulate transcription factors NF-kappa B, AP-1 and Egr-1; down-regulate the expression of COX2, LOX, NOS, MMP-9, uPA, TNF, chemokines, cell surface adhesion molecules and cyclin D1; down-regulate growth factor receptors (such as EGFR and HER2); and inhibit the activity of c-Jun N-terminal kinase, protein tyrosine kinases and protein serine/threonine kinases. In several systems, curcumin has been described as a potent antioxidant and anti-inflammatory agent. Evidence has also been presented to suggest that curcumin can suppress tumor initiation, promotion and metastasis. Pharmacologically, curcumin has been found to be safe. Human clinical trials indicated no dose-limiting toxicity when administered at doses up to 10 g/day. All of these studies suggest that curcumin has enormous potential in the prevention and therapy of cancer. The current review describes in detail the data supporting these studies.
Robust hepatitis C virus infection in vitro (2005)

The absence of a robust cell culture model of hepatitis C virus (HCV) infection has severely limited analysis of the HCV life cycle and the development of effective antivirals and vaccines. Here we report the establishment of a simple yet robust HCV cell culture infection system based on the HCV JFH-1 molecular clone and Huh-7-derived cell lines that allows the production of virus that can be efficiently propagated in tissue culture. This system provides a powerful tool for the analysis of host-virus interactions that should facilitate the discovery of antiviral drugs and vaccines for this important human pathogen.
Regulation of activated protein C by protein S. The role of phospholipid in factor Va inactivation. (1981)

Protein S enhances the rate of Factor Va inactivation by activated Protein C (Walker, F. J. (1980) J. Biol. Chem. 255, 5521-5524). The activity of protein S is saturable, appearing to interact stoichiometrically with activated Protein C. Diisopropylphosphate-modified activated Protein C reversed the effect of Protein S, further indicating that a Protein S-activated Protein C interaction is required for expression of the activity of Protein S. In the absence of phospholipid, Protein S had no effect on the rate of activated Protein C-catalyzed inactivation of Factor Va. The activity of Protein S was only expressed in the presence of phospholipid vesicles, where it appeared to increase the affinity of the inactivation system for phospholipid. Protein S had no effect upon the rate of Factor Va inactivation in the presence of saturating levels of phospholipid vesicles. The effects of Protein S on the kinetics of Factor Va inactivation corresponded with its effect on the interaction between activated Protein C and phospholipid vesicles, measured by light scattering. In the presence of Protein S, the binding of activated Protein C to phospholipid vesicles was enhanced. Protein S had no effect upon the binding on the zymogen (Protein C to phospholipid vesicles). In conclusion, the stimulatory effect of Protein S on the inactivation of Factor Va by activated Protein C can be attributed, in part, to the enhancement of the binding of activated Protein C to phospholipid vesicles.
Dynamic regulation of ERK2 nuclear translocation and mobility in living cells (2006)

The extracellular signal-regulated protein kinase ERK1/2 is a crucial effector linking extracellular stimuli to cellular responses: upon phosphorylation ERK [also known as mitogen-activated protein kinase P42/P44 (MAPK)] concentrates in the nucleus where it activates specific programs of gene expression. Notwithstanding the importance of this process, little is known about the modalities, time course and regulation of ERK exchange between nucleus and cytoplasm in living cells. We visualized the dynamic of nuclear translocation by expressing low levels (&amp;lt;150 nM) of fluorescently tagged ERK2 in living fibroblasts. Time-lapse imaging demonstrated that nuclear concentration can change bidirectionally with a time constant of a few minutes. The increase of nuclear concentration requires continuous MEK (also known as MAPK kinase) activity upstream of ERK and is rapidly reduced by the operation of phosphatases. We measured quantitatively the speed of ERK2 shuttling between nucleus and cytoplasm and determined that shuttling accelerated after ERK activation, becoming fast enough not to be rate-limiting for translocation. Finally, we demonstrated that ERK2 did not diffuse freely in the nucleus and that diffusion was further impeded after phosphorylation, suggesting the formation of complexes of low mobility. These results show that nucleocytoplasmic trafficking of ERK2 and its mobility are dynamically regulated in living cells.
Phosphoramidate Derivatives of Stavudine as Inhibitors of HIV: Unnatural Amino Acids May Substitute for Alanine (2000)

Some novel phosphoramidate derivatives of the nucleoside analogue stavudine have been prepared as membrane-soluble prodrugs of the bioactive free phosphate forms. Phenyl phosphates linked via nitrogen to methyl esterified amino acid analogues were studied, where the amino acid was an unnatural alpha-alkyl (or aryl) glycine or an alpha,alpha-dialkyl glycine. All compounds were characterized by a range of spectroscopic, spectrometric and analytical methods and were subjected to in vitro evaluation of their anti-human immunodeficiency virus efficacy. It is notable that certain unnatural amino acid derivatives could substitute for alanine with only a relatively small loss of activity and, moreover, that this activity did not fall-off with increasing alkyl chain length for the C2-C4 mono-alkyl series. These data are further probed by the application of our recently reported 31P-NMR-based carboxyl esterase assay, with informative results.
The Hydrophobic Face Orientation of Apolipoprotein A-I Amphipathic Helix Domain 143–164 Regulates Lecithin:Cholesterol Acyltransferase Activation (1998)

Apolipoprotein A-I (apoA-I) activates the plasma enzyme lecithin:cholesterol acyltransferase (LCAT), catalyzing the rapid conversion of lipoprotein cholesterol to cholesterol ester. Structural mutants of apoA-I have been used to study the details of apoA-I-LCAT-catalyzed cholesterol ester formation. Several studies have shown that the alpha-helical segments corresponding to amino acids 143-164 and 165-186 (repeats 6 and 7) are essential for LCAT activation. In the present studies, we examined how the orientation of the hydrophobic face, independent of an increase in overall hydrophobicity, affects LCAT activation. We designed, expressed, and characterized a mutant, reverse of 6 apoA-I (RO6 apoA-I), in which the primary amino acid sequence of repeat 6 (amino acids 143-164) was reversed from its normal orientation. This mutation rotates the hydrophobic face of repeat 6 approximately 80 degrees. Lipid-free RO6 apoA-I showed a marked stabilization when denatured by guanidine hydrochloride, but showed significant destabilization to guanidine hydrochloride denaturation in the lipid-bound state compared with wild-type apoA-I. Recombinant high density lipoprotein discs (rHDL) formed from RO6 apoA-I, sn-1-palmitoyl-sn-2-oleoyl phosphati-dylcholine, and cholesterol were approximately 12 A smaller than wild-type apoA-I rHDL. The reduced size suggests that one of the repeats did not effectively participate in phospholipid binding and organization. The sn-1-palmitoyl-sn-2-oleoyl phosphatidylcholine RO6 rHDL were a less effective substrate for LCAT. Mapping the entire lipid-free and lipid-bound RO6 apoA-I with a series of monoclonal antibodies revealed that both the lipid-free and lipid-bound RO6 apoA-I displayed altered or absent epitopes in domains within and adjacent to repeat 6. Together, these results suggest that the proper alignment and orientation of the hydrophobic face of repeat 6 is an important determinant for maintaining and stabilizing helix-bilayer and helix-helix interactions.
Production of glycosylated physiologically "normal" human alpha 1-antitrypsin by mouse fibroblasts modified by insertion of a human alpha 1-antitrypsin cDNA using a retroviral vector. (1987)

Alpha 1-Antitrypsin (alpha 1AT) deficiency is a hereditary disorder characterized by reduced serum levels of alpha 1AT, resulting in destruction of the lower respiratory tract by neutrophil elastase. As an approach to augment alpha 1AT levels in this disorder with physiologically normal human alpha 1AT, we have integrated a full-length normal human alpha 1AT cDNA into the genome of mouse fibroblasts. To accomplish this, the retroviral vector N2 was modified by inserting the simian virus 40 early promoter followed by the alpha 1AT cDNA. Southern analysis demonstrated that the intact cDNA was present in the genome of selected clones of the transfected murine fibroblasts psi 2 and infected NIH 3T3. The clones produced three mRNA transcripts (5.8, 4.8, and 2.4 kilobases) containing human alpha 1AT sequences, secreted an alpha 1AT molecule recognized by an anti-human alpha 1AT antibody, with the same molecular mass (52 kDa) as normal human alpha 1AT and that complexed with and inhibited human neutrophil elastase. The psi 2 produced alpha 1AT was glycosylated, and when infused intravenously into mice, it had a serum half-life similar to normal alpha 1AT purified from human plasma and markedly longer than that of nonglycosylated human alpha 1AT cDNA-directed yeast-produced alpha 1AT. These studies demonstrate the feasibility of using a retroviral vector to insert the normal human alpha 1AT cDNA into non-alpha 1AT-producing cells, resulting in the synthesis and secretion of physiologically "normal" human alpha 1AT.
Time-resolved optical gating based on dispersive propagation: a new method to characterize optical pulses (2000)

We introduce the technique of time-resolved optical gating (TROG) based on dispersive propagation (DP), a new noninterferometric method for characterizing ultrashort optical pulses in amplitude and phase without the need for a short optical gating pulse. TROG is similar to frequency-resolved optical gating except that the role of time and frequency is interchanged. For the DP-TROG geometry, we show that measurements of the autocorrelation trace of the pulse after propagation through a medium with variable dispersion together with a single measurement of its intensity spectrum contain sufficient information to reconstruct the pulse in amplitude and phase. Pulse reconstruction for this DP-TROG geometry works very well even for the case of a nonlinearly chirped double pulse. Compared with other methods, DP-TROG does not introduce an ambiguity in the direction of time for the pulse. Due to its simplicity and improved sensitivity. DP-TROC is expected to be useful in characterizing low-energy pulses.
Hypertension Induced Alterations in Copper and Zinc Metabolism: A Link to Vascular Disease? (1987)

Ischemic heart disease is the leading cause of death in the United States and other industrialized countries. Although the etiology of disease is without question multifactorial in nature, several potential risk factors have been agreed upon. These risk factors include hypercholesterolemia, hypertension, electrocardiogram abnormalities, cigarette smoking and diabetes.1 During the last decade it has been proposed that Cu deficiency may also be a significant risk factor for vascular disease. This hypothesis has been based on the observations that severe Cu deficiency in experimental and domestic animals can result in connective tissue defects producing myocardial damage and aortic aneurysms, and that the dietary intake of Cu is often below that suggested by health agencies.2,3 Furthermore, the risk of Cu deficiency is thought to be increased by the consumption of excess Zn in the diet, as these two elements can be biologically antagonistic.3–5
Morphogenesis of rabbit corneal stroma. (1983)

Corneas of fetal and young albino rabbits were examined by light and transmission electron microscopy. In addition, DNA and hydroxyproline content were measured in developing stroma. The results were compared with similar data from healing corneas in adult rabbits and from developing corneas of other animal species. In the fetal rabbit, the prospective corneal stroma region contains an unorganized, sparse extracellular matrix until about the 13th day of gestation, when mesenchymal cells and capillaries from the hyaloid vessels move in to form the vascular pupillary membrane, endothelium, and stroma. Stromal growth is due to alteration in the density and morphology of the cell population early in development, along with a sequential thickening and thinning of the whole stroma. These events are similar to those reported in primates, but differ markedly from those reported in avian species. Normal developing cornea and healing adult cornea both involve migration of stomal fibroblasts and deposition of extracellular matrix. Stromal fibroblasts in the rabbit fetus are oriented with their long axis parallel to the corneal surface early in development compared with randomly oriented fibroblasts in the early healing wound of adult rabbit corneas. Although collagen and cell number progressively increase throughout the developmental periods studied, the ratio of cells to collagen is high initially but decreases with development. In contrast, the proportion of cells to collagen in the young scar tissue of adult cornea is low initially, indicating a marked deposition of collagen in comparison to that in the early normal developing stroma. The results suggest that the healing tissue differs from the normal fetal stroma in its coordination of cell population growth with collagen deposition and cellular organization.
Expression of a cDNA encoding a functional 241-kilodalton vesicular stomatitis virus RNA polymerase. (1985)

The large gene, L, of vesicular stomatitis virus (VSV), which codes for the multifunctional RNA-dependent RNA polymerase, was assembled from five overlapping cDNA clones. The sequence of the 6.4-kilobase gene of the final construct was identical to the consensus sequence reported earlier. The gene was inserted into the simian virus 40 transient expression vector pJC119. Antibodies directed against synthetic peptides corresponding to the amino and carboxyl termini of the L protein were raised in rabbits. Both antibodies specifically immunostained the cytoplasm of COS cells that had been transfected with the vector DNA. The expressed L protein was immunoprecipitated from cell extracts and it was identical in size to the L protein of the virion (241 kilodaltons). Most importantly, COS cells that expressed the recombinant L protein transcribed, replicated, and consequently complemented and rescued temperature-sensitive RNA polymerase mutants of VSV at the nonpermissive temperature. The kinetics of virus release were similar to those of a wild-type VSV infection. We conclude that the recombinant RNA polymerase protein L is indistinguishable in its size and its functions from the VSV polymerase.
A retrospective on the Dorado, a high-performance personal computer (1983)

In late 1975, members of the Xerox Palo Alto Research Center embarked on the specification of a high-performance successor to the Alto personal minicomputer, in use since 1973. After four years, the resulting machine, called the Dorado, was in use within the research community at PARC. This paper begins with an overview of the design goals, architecture, and implementation of the Dorado and then provides a retrospective view and critique of the Dorado project as a whole. The major machine architectural features are evaluated, other project aspects such as design automation and management structures are explained, a chronological history with milestones is included, and a variety of accomplishments, red herrings, and shortfalls is discussed. The paper concludes with some speculations on what the project might have done differently and what might be done differently today instead of in the late 1970s. Although more than a dozen scientists and technicians contributed to the project, the evaluative and speculative parts of this paper are the sole responsibility of the author.
Expression of BAG-1 in Invasive Breast Carcinomas (1999)

BAG-1 is overexpressed in the majority of invasive breast carcinomas. Although BAG-1 did not correlate with conventional prognostic factors, its overexpression, especially the nuclear expression, may be associated with a shorter disease-free and overall survival. Our preliminary data strongly indicate that further investigation is warranted to define the role of BAG-1 as an independent prognostic factor in patients with newly diagnosed breast cancer.
Targeted delivery of CRISPR/Cas9 to prostate cancer by modified gRNA using a flexible aptamer-cationic liposome (2016)

The potent ability of CRISPR/Cas9 system to inhibit the expression of targeted gene is being exploited as a new class of therapeutics for a variety of diseases. However, the efficient and safe delivery of CRISPR/Cas9 into specific cell populations is still the principal challenge in the clinical development of CRISPR/Cas9 therapeutics. In this study, a flexible aptamer-liposome-CRISPR/Cas9 chimera was designed to combine efficient delivery and increased flexibility. Our chimera incorporated an RNA aptamer that specifically binds prostate cancer cells expressing the prostate-specific membrane antigen as a ligand. Cationic liposomes were linked to aptamers by the post-insertion method and were used to deliver therapeutic CRISPR/Cas9 that target the survival gene, polo-like kinase 1, in tumor cells. We demonstrate that the aptamer-liposome-CRISPR/Cas9 chimeras had a significant cell-type binding specificity and a remarkable gene silencing effect in vitro. Furthermore, silencing promoted a conspicuous regression of prostate cancer in vivo. Importantly, the approach described here provides a universal means of cell type-specific CRISPR/Cas9 delivery, which is a critical goal for the widespread therapeutic applicability of CRISPR/Cas9 or other nucleic acid drugs.