gebhart/patrepeval huggingface dataset:
A high-throughput microscale method to release N-linked oligosaccharides from glycoproteins for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis (1998)

This report describes a convenient method for the rapid and efficient release of N-linked oligosaccharides from low microgram amounts of glycoproteins. A 96-well MultiScreen assay system containing a polyvinylidene difluoride (PVDF) membrane is employed to immobilize glycoproteins for subsequent enzymatic deglycosylation. Recombinant tissue-type plasminogen activator (rt-PA) is used to demonstrate the deglycosylation of 0.1-50 micrograms of a glycoprotein. This method enabled the recovery of a sufficient amount of N-linked oligosaccharides released enzymatically with peptide N-glycosidase F (PNGaseF) from as little as 0.5 microgram rt-PA for subsequent analysis by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The immobilization of rt-PA to the PVDF membrane did not sterically inhibit the PNGaseF-mediated release of oligosaccharides from rt-PA as determined by tryptic mapping experiments. Comparison of the oligosaccharides released from 50 micrograms of rt-PA by either the 96-well plate method or by a standard solution digestion procedure showed no significant differences in the profiles obtained by high-pH anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). Both neutral and sialylated oligosaccharide standards spiked into wells were recovered equally as determined by HPAEC-PAD. One advantage of this approach is that reduction and alkylation can be performed on submicrogram amounts of glycoproteins with easy removal of reagents prior to PNGaseF digestion. In addition, this method allows 60 glycoprotein samples to be deglycosylated in 1 day with MALDI-TOF or HPAEC-PAD analysis being performed on the following day.
Ketogenic Essential Amino Acids Modulate Lipid Synthetic Pathways and Prevent Hepatic Steatosis in Mice (2010)

Our results indicate that dietary KAA intake improves hepatic steatosis and insulin resistance by modulating lipid synthetic pathways.
First 100% Reuse of Bakken Produced Water in Hybrid Treatments Using Inexpensive Polysaccharide Gelling Agents (2015)

Abstract The modern horizontal multistage well is a main contributor to the recent transformation of North American oil and gas production. The large fracturing stage volume that defines unconventional wells, crossed against the increasing numbers of stages and laterals per pad, has dramatically increased the demand for fracturing materials such as sand, friction reducers, and gelling agents, and most especially water. At the same time, operators face increasing accumulations of produced water, which presents as water cut from more mature assets. It is therefore natural to propose using produced water as mixwater for fracturing fluids in new completions, but in practice this plan has met with two major barriers: first, regulatory and logistical hurdles concerning the storage, handling, and potential environmental impacts of the volume of produced water required to complete a modern well (millions of gallons per lateral), and second, technology gaps in the applied chemistry of completion fluids, particularly in crosslinked gels. This paper reports the completion of a two-lateral well in the Williston Basin where produced water, filtered but otherwise untreated, was used throughout the slickwater and crosslinked components of about sixty hydraulic fracturing stages. Proppant was successfully placed in all perforated zones in the Bakken and Three Forks formations, using a “hybrid” design that employed seven million gallons of water (of which 2.2 million gallons were crosslinked). Production figures for the well are satisfactory, and this is discussed in the context of fluid-related completion quality. This paper will concentrate on the development and implementation of a metal crosslinked fracturing fluid that shows excellent stability at typical Bakken conditions. We will present a comparison to conventional guar-borate systems. The promise of this approach has many potential benefits. First, completion costs are decreased as freshwater sourcing and produced water disposal charges cancel each other. Second, far fewer truck trips are necessary to transport water. Third, the industry no longer requires fresh water sources or disposal wells where this technique is employed.
Severe CD4+T-Cell Depletion in Gut Lymphoid Tissue during Primary Human Immunodeficiency Virus Type 1 Infection and Substantial Delay in Restoration following Highly Active Antiretroviral Therapy (2003)

Gut-associated lymphoid tissue (GALT) harbors the majority of T lymphocytes in the body and is an important target for human immunodeficiency virus type 1 (HIV-1). We analyzed longitudinal jejunal biopsy samples from HIV-1-infected patients, during both primary and chronic stages of HIV-1 infection, prior to and following the initiation of highly active antiretroviral therapy (HAART) to determine the onset of CD4(+) T-cell depletion and the effect of HAART on the restoration of CD4(+) T cells in GALT. Severe depletion of intestinal CD4(+) T cells occurred during primary HIV-1 infection. Our results showed that the restoration of intestinal CD4(+) T cells following HAART in chronically HIV-1-infected patients was substantially delayed and incomplete. In contrast, initiation of HAART during early stages of infection resulted in near-complete restoration of intestinal CD4(+) T cells, despite the delay in comparison to peripheral blood CD4(+) T-cell recovery. DNA microarray analysis of gene expression profiles and flow-cytometric analysis of lymphocyte homing and cell proliferation markers demonstrated that cell trafficking to GALT and not local proliferation contributed to CD4(+) T-cell restoration. Evaluation of jejunal biopsy samples from long-term HIV-1-infected nonprogressors showed maintenance of normal CD4(+) T-cell levels in both GALT and peripheral blood. Our results demonstrate that near-complete restoration of mucosal immune system can be achieved by initiating HAART early in HIV-1 infection. Monitoring of the restoration and/or maintenance of CD4(+) T cells in GALT provides a more accurate assessment of the efficacy of antiviral host immune responses as well as HAART.
Constitutive and regulated α-secretase cleavage of Alzheimer’s amyloid precursor protein by a disintegrin metalloprotease (1999)

Amyloid beta peptide (Abeta), the principal proteinaceous component of amyloid plaques in brains of Alzheimer's disease patients, is derived by proteolytic cleavage of the amyloid precursor protein (APP). Proteolytic cleavage of APP by a putative alpha-secretase within the Abeta sequence precludes the formation of the amyloidogenic peptides and leads to the release of soluble APPsalpha into the medium. By overexpression of a disintegrin and metalloprotease (ADAM), classified as ADAM 10, in HEK 293 cells, basal and protein kinase C-stimulated alpha-secretase activity was increased severalfold. The proteolytically activated form of ADAM 10 was localized by cell surface biotinylation in the plasma membrane, but the majority of the proenzyme was found in the Golgi. These results support the view that APP is cleaved both at the cell surface and along the secretory pathway. Endogenous alpha-secretase activity was inhibited by a dominant negative form of ADAM 10 with a point mutation in the zinc binding site. Studies with purified ADAM 10 and Abeta fragments confirm the correct alpha-secretase cleavage site and demonstrate a dependence on the substrate's conformation. Our results provide evidence that ADAM 10 has alpha-secretase activity and many properties expected for the proteolytic processing of APP. Increases of its expression and activity might be beneficial for the treatment of Alzheimer's disease.
Comparison of In Vitro Anticancer-Drug-Screening Data Generated With a Tetrazolium Assay Versus a Protein Assay Against a Diverse Panel of Human Tumor Cell Lines (1990)

The National Cancer Institute (NCI) is implementing a large-scale in vitro drug-screening program that requires a very efficient automated assay of drug effects on tumor cell viability or growth. Many laboratories worldwide have adopted a microculture assay based on metabolic reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). However, because of certain technical advantages to use of the protein-binding dye sulforhodamine B (SRB) in a large-scale screening application, a detailed comparison of data generated by each type of assay was undertaken. The MTT and SRB assays were each used to test 197 compounds, on simultaneous days, against up to 38 human tumor cell lines representing seven major tumor categories. On subsequent days, 38 compounds were retested with the SRB assay and 25 compounds were retested with the MTT assay. For each of these three comparisons, we tabulated the differences between the two assays in the ratios of test group values to control values (T/C) for cell survival; calculated correlation coefficients for various T/C ratios; and estimated the bivariate distribution of the values for IC50 (concentration of drug resulting in T/C values of 50%, or 50% growth inhibition) for the two assays. The results indicate that under the experimental conditions used and within the limits of the data analyses, the assays perform similarly. Because the SRB assay has practical advantages for large-scale screening, however, it has been adopted for routine use in the NCI in vitro antitumor screen.
Chemokine stimulation of monocyte matrix metalloproteinase-9 requires endogenous TNF-α (2002)

Leukocyte extravasation into tissues is a multi-step process culminating in the migration of cells through the basement membrane. This requires the production of matrix-degrading enzymes, in particular matrix metalloproteinases (MMP). We investigated the role of chemokines in regulating MMP production in the monocytic cell line THP-1 and in peripheral blood monocytes (PBM). The CC chemokines CCL2 (MCP-1), CCL3 (MIP-1alpha), and CCL5 (RANTES) stimulated the release of monocyte MMP-9 protein in a bell-shaped dose-dependent manner. The increase in MMP-9 protein detected at 24 h was due to de novo synthesis, confirmed by Northern blotting, with MMP-9 mRNA detectable at 6-8 h. Autocrine TNF-alpha was necessary for chemokine stimulation of MMP-9. Chemokines increased TNF-alpha mRNA levels and protein release in monocytes and THP-1 cells, and neutralizing anti-TNF-alpha antibodies inhibited CCL2-induced MMP-9 release. Furthermore, the broad spectrum MMP inhibitor BB 2516, which inhibits TNF-alpha release, abrogated CCL2- and CCL5-induced MMP-9 release in both THP-1 cells and freshly isolated monocytes. Monocyte production of MMP is of major importance in the pathology of cancer, asthma, and rheumatoid arthritis. An understanding of the mechanisms by which these MMP are produced may lead to novel therapies to modulate extravasation of leukocytes in disease.
Reduced Foveolar Choroidal Blood Flow in Eyes with Increasing AMD Severity (2005)

There is a systematic decrease in choroidal circulatory parameters with an increase in the severity of AMD features associated with risk for the development of CNV, suggesting a role for ischemia in the development of CNV.
Total Synthesis of Himastatin: Confirmation of the Revised Stereostructure (1998)

A stereoisomer of the natural product and not himastatin, an unusual dimeric depsipeptide with promising antibiotic and antitumor properties, was obtained from pyrroloindoline anti-cis-1. This result led to a revision of the proposed stereostructure. The new stereostructure was confirmed by the total synthesis, which involves stereoselective access to the pyrroloindoline syn-cis-1 and the 5-hydroxypiperazic acid subunit and features a Stille coupling for the formation of the central carbon-carbon bond.
Graft-versus-leukemia effect after allogeneic bone marrow transplantation for chronic lymphocytic leukemia. (1996)

We report the case of a patient with chronic lymphocytic leukemia (CLL) with persistent lymphocytosis and lymphadenopathy after allogeneic bone marrow transplantation (BMT). After receiving a donor lymphocyte infusion on day 87 he achieved complete remission upon development of chronic graft-versus-host disease, suggesting that a graft-versus-leukemia effect is operative in this malignancy.
Predictive and prognostic value of preoperative serum tumor markers in resectable adenosqamous lung carcinoma (2016)

Adenosquamous lung carcinoma is an aggressive malignancy with relatively high EGFR mutation frequency. Elevated preoperative NSE level and TMI are adverse predictive and prognostic indicators.
Direct Colorimetric Detection of a Receptor-Ligand Interaction by a Polymerized Bilayer Assembly (1993)

Detection of receptor-ligand interactions is generally accomplished by indirect assays such as enzyme-linked immunosorbent assay. A direct colorimetric detection method based on a polydiacetylene bilayer assembled on glass microscope slides has been developed. The bilayer is composed of a self-assembled monolayer of octadecylsilane and a Langmuir-Blodgett monolayer of polydiacetylene. The polydiacetylene layer is functionalized with an analog of sialic acid, the receptor-specific ligand for the influenza virus hemagglutinin. The sialic acid ligand serves as a molecular recognition element and the conjugated polymer backbone signals binding at the surface by a chromatic transition. The color transition is readily visible to the naked eye as a blue to red color change and can be quantified by visible absorption spectroscopy. Direct colorimetric detection by polydiacetylene films offers new possibilities for diagnostic applications and screening for new drug candidates or binding ligands.
DNA-dependent RNA polymerase from bacteriophage N4 virions. Purification and characterization. (1980)

A DNA-dependent RNA polymerase has been purified to homogeneity from bacteriophage N4 virions. Sodium dodecyl sulfate-8 M urea polyacrylamide gel electrophoresis of the enzyme revealed a single polypeptide with a molecular weight of 350,000. The hydrodynamic properties of the enzyme have been determined to be 9.5 S for the sedimentation coefficient and 84 A for the Stokes radius. These two parameters indicate a native molecular weight of 320,000. Enzyme activity is dependent on the presence of Mg2+, the four ribonucleoside triphosphates, and denatured N4 DNA. Under these conditions, initiation of RNA synthesis occurs exclusively with pppG. The enzyme is inhibited by monovalent salts and is resistant to the drugs rifampicin and streptolydigin. The protein is present in 1 to 2 copies per virion; its presence provides an explanation for the independence of N4 early RNA synthesis on the activity of the host RNA polymerase.
Holographic solar concentrator (1982)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Jacques E. Ludman, "Holographic solar concentrator," Appl. Opt. 21, 3057-3058 (1982) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex (2018)

Transcription activation domains (ADs) are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription activation by yeast Gcn4 requires its tandem ADs and four activator-binding domains (ABDs) on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous and contains nearly all possible AD-ABD interactions. Gcn4-Med15 forms via a dynamic fuzzy protein-protein interface, where ADs bind the ABDs in multiple orientations via hydrophobic regions that gain helicity. This combinatorial mechanism allows individual low-affinity and specificity interactions to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators, as it allows great flexibility in combinations of activators that can cooperate to regulate genes with variable coactivator requirements.
Failure modes for stiction in surface-micromachined MEMS (2002)

Wafer-level testing of surface-micromachined sensors provides new challenges to the test community. Currently, there is no method available for performing direct measurements to assess faulty micromechanical structures. Most commercial methods use electrical measurements to deduce the physical source of failures in the micromechanical structure. As a result, the process of identifying various failure modes (electrical measurements) and accurately mapping them to the underlying physical failure mechanisms of the mechanical sensor becomes highly complex. Several sources of failures that include particulates and stiction complicate the situation even more. Here, we provide a case study of the Analog Devices ADXL75 Accelerometer. One failure category called stuck/tipped beams is investigated and a methodology is developed to uniquely distinguish failures either caused by stuck or tipped beams. The proposed method is easy to implement and the information obtained can be critical for yield improvement.
The B-type natriuretic peptide assay: a rapid test for heart failure. (2002)

The B-type or brain natriuretic peptide (BNP) assay, a 15-minute bedside blood test, is highly sensitive and fairly specific for diagnosing heart failure and is useful in evaluating suspected heart failure in outpatients and in emergency care. Other uses include screening for left ventricular dysfunction and predicting outcome in patients with an established diagnosis of heart failure or myocardial infarction.
Tip–sample forces in scanning probe microscopy in air and vacuum (1992)

Forces between a probe and sample have been measured in air and vacuum using a rocking beam force balance sensor capable of simultaneously obtaining both force and tunneling topographs. Force versus distance curve measurements demonstrate the effects of capillary forces in air but not in vacuum. Simultaneous scanning tunneling microscope (STM) imaging and force measurement in air show spatial force variations consistent with repulsive force tunneling. Our results support observations of large repulsive forces in STM occurring from surface contaminants. These results show how forces can affect image formation in both STM and scanning force microscopy.
A Position Effect on the Expression of a tRNA Gene Mediated by the SIR Genes in Saccharomyces cerevisiae (1986)

The SIR genes of Saccharomyces cerevisiae are responsible for the position-dependent regulation of the a and alpha mating-type genes. Previous work by others has shown that the products of the SIR genes prevent the accumulation of stable transcripts of the a and alpha genes at HML and HMR. Results of this study establish that this regulation is a region-specific effect rather than a gene-specific effect since expression of a tRNA gene placed at HMR is repressed by the products of the SIR genes.
Molecular Mechanism of Oil Shale Pyrolysis in Nitrogen and Hydrogen Atmospheres (1983)

This paper describes the changes in carbon functionality that occur during the pyrolysis and hydropyrolysis of Colorado oil shale. This paper is different from earlier work in that characterization of shale and products is combined with highly mass-balanced reactions to allow a mechanistic discussion of the role of functionalities in the generation of oil during shale pyrolysis. We identify some important factors in maximizing the conversion of kerogen to oil. Colorado oil shale was pyrolyzed under conditions of slow heatup (6°C/min) and short gas residence times (2-4 sec) in a nitrogen or hydrogen atmosphere at 2600 kPa. Product characterization was by elemental analysis, GC (gas), and NMR (solid & liquid). The aliphatic portion of the shale either cracks to give oil and gas or aromatizes to give aromatics in the oil or spent shale. There is an 80% increase in aromatic carbon during pyrolysis. The aromatic portion of the kerogen either cracks to give oil or ends up in the spent shale. Mineral carbonates, rather than organic functionalities, are the source of most of the CO2. Hydrogen is effective at inhibiting the reactions which lead to aromatization and formation of residual carbon. Molecular hydrogen in the system also reduces carbonates to methane and water.
Inhibiton of IL 2 production after human allogeneic bone marrow transplantation. (1983)

Bone marrow transplantation (BMT) is currently used to treat patients with severe aplastic anemia or leukemia. Despite the use of an HLA identical sibling donor, however, the survival after BMT is reduced by the occurrence of two major immunologic complications: graft-vs-host disease and a long-lasting immune deficiency responsible for late infections. This immune deficiency could be explained by an imbalance of lymphocyte subpopulations reconstituted after transplant. The aim of the present work was to study the helper function by measuring the production of interleukin 2 (IL 2). This lymphokine is responsible for the amplification of the effector phase of immunity. A consecutive series of 34 patients was tested for IL 2 production after BMT. This production was absent or low in 32 of 34 patients for at least 2 yr after BMT. The mechanism of this low IL 2 production was investigated. Irradiation of patients' lymphocytes in vitro with low dose gamma-rays partially restored the IL 2 production after 6 mo of evolution. The IL 2 production was not restored or was slightly affected by irradiation early after BMT. These results suggest that the lack of immune reconstitution after BMT may be caused by the lack of IL 2-producing cells and/or the increased activity of suppressor cells of the helper function. This suppression is radiosensitive.
Pyrimidine Thioethers:  A Novel Class of HIV-1 Reverse Transcriptase Inhibitors with Activity Against BHAP-Resistant HIV (1998)

A series of pyrimidine thioethers was synthesized and evaluated for inhibitory properties against wild-type HIV-1 reverse transcriptase (RT) and an RT carrying the resistance-conferring mutation P236L. Modifications of both the pyrimidine and the functionality attached through the thioether yielded several analogues, which demonstrated activity against both enzyme types, with IC50 values as low as 190 nM against wild-type and 66 nM against P236L RT. Evaluation of a select number of pyrimidine thioethers in cell culture showed that these compounds have excellent activity against HIV-1IIIB-WT and retain good activity against a laboratory-derived HIV-1MF delavirdine-resistant variant.
Recombinant fusion proteins TAT‐Mu, Mu and Mu‐Mu mediate efficient non‐viral gene delivery (2007)

Recombinant proteins that are heterologous fusions, having DNA-binding domains and nuclear localization epitopes, generated in this study have considerable potential to facilitate DNA delivery and enhance transfection. The domains in these fusion proteins would be promising in the development of non-viral gene delivery vectors particularly in cells that do not divide.