gebhart/patrepeval huggingface dataset:
Fluorescent Chemosensors for Divalent Zinc Based on Zinc Finger Domains. Enhanced Oxidative Stability, Metal Binding Affinity, and Structural and Functional Characterization (1997)

The design, synthesis, and characterization of a family of peptides modeled after the zinc finger domains, which has led to the production of a fluorescent peptidyl sensor for divalent zinc with enhanced oxidative stability, are reported. The chemosensor design comprises a synthetic peptidyl template and a covalently attached fluorescent reporter which is sensitive to metal-induced conformational changes in the polypeptide construct. The modular synthetic approach employed for the construction of these chemosensors allows independent modification of the metal coordination sphere and the fluorescent reporter group. The structural, fluorescence, and zinc binding properties of these peptides and the effects of integrating various environment sensitive fluorophores, 4-(dimethylamino)benzamide, 5-(dimethylamino)naphthalenesulfonamide, and 3-carboxamidocoumarin, are described. Manipulation of the ligand sphere, by removal of one of the pair of thiolate ligands, was undertaken to enhance the oxidative stability of the chemosensor. For each of these peptides, the apparent dissociation constant of the peptide−zinc complex has been determined by spectroscopic methods. High-affinity binding, with dissociation constants ranging from 7 pM to 65 nM, is observed.
Liquid chromatography mass spectrometry-based proteomics: Biological and technological aspects (2010)

Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used, significant challenges remain, and there are many opportunities for statisticians to make important contributions. In the most widely used "bottom-up" approach to proteomics, complex mixtures of proteins are first subjected to enzymatic cleavage, the resulting peptide products are separated based on chemical or physical properties and analyzed using a mass spectrometer. The two fundamental challenges in the analysis of bottom-up MS-based proteomics are: (1) Identifying the proteins that are present in a sample, and (2) Quantifying the abundance levels of the identified proteins. Both of these challenges require knowledge of the biological and technological context that gives rise to observed data, as well as the application of sound statistical principles for estimation and inference. We present an overview of bottom-up proteomics and outline the key statistical issues that arise in protein identification and quantification.
Layout optimization of cascode RF SOI transistors (2002)

Two different layouts of two MOSFETs connected in cascode were studied. The measured results were compared to simulations.
Auctions with Budget-Constrained Buyers : A Nonequivalence Result (1994)

Anecdotal evidence of concern about the limited financial resources of small firms abounds in government auctions. Recent empirical work also provides evidence of the importance of capital constraints. In this paper, we show that the first-price sealed-bid auction yields higher expected revenue than the second-price sealed-bid auction if buyers face wealth constraints. Differences in the extent to which wealth constraints bind in the different auction formats generate the revenue nonequivalence.
A Glycophospholipid Tail at the Carboxyl Terminus of the Thy-1 Glycoprotein of Neurons and Thymocytes (1985)

Cell surface molecules of eukaryotic cells have been considered to be integrated into the membrane bilayer by a transmembrane protein sequence. The Thy-1 antigen of rodent thymocytes and brain was the first eukaryotic membrane molecule for which biochemical data clearly suggested membrane integration via a nonprotein tail. Direct evidence is now presented showing that a glycophospholipid structure is attached to the carboxyl-terminal cysteine residue and that 31 carboxyl-terminal amino acids predicted from the Thy-1 complementary DNA sequence are not present in the mature glycoprotein. These experimental results raise questions concerning signaling across a cell membrane since antibodies to Thy-1 can stimulate T lymphocytes to release lymphokines and undergo cell division.
Protein secretion and surface display in Gram-positive bacteria (2012)

The cell wall peptidoglycan of Gram-positive bacteria functions as a surface organelle for the transport and assembly of proteins that interact with the environment, in particular, the tissues of an infected host. Signal peptide-bearing precursor proteins are secreted across the plasma membrane of Gram-positive bacteria. Some precursors carry C-terminal sorting signals with unique sequence motifs that are cleaved by sortase enzymes and linked to the cell wall peptidoglycan of vegetative forms or spores. The sorting signals of pilin precursors are cleaved by pilus-specific sortases, which generate covalent bonds between proteins leading to the assembly of fimbrial structures. Other precursors harbour surface (S)-layer homology domains (SLH), which fold into a three-pronged spindle structure and bind secondary cell wall polysaccharides, thereby associating with the surface of specific Gram-positive microbes. Type VII secretion is a non-canonical secretion pathway for WXG100 family proteins in mycobacteria. Gram-positive bacteria also secrete WXG100 proteins and carry unique genes that either contribute to discrete steps in secretion or represent distinctive substrates for protein transport reactions.
Recombinant human Fab to glycoprotein D neutralizes infectivity and prevents cell-to-cell transmission of herpes simplex viruses 1 and 2 in vitro. (1994)

Herpes simplex viruses 1 and 2 (HSV-1 and -2) are associated with a number of conditions of varying severity, which are only partially responsive to current therapies. Human antibodies to the viruses offer a potential alternative. We describe here the generation of panels of human monoclonal Fab fragments to HSV-1 and -2 by panning a phage display combinatorial antibody library against whole lysates from the two viruses. Each lysate selected a largely distinct set of Fabs, although all of the Fabs were cross-reactive with both viruses. In a plaque-reduction assay, one Fab neutralized HSV-1 at 0.25 microgram/ml (50% reduction) and HSV-2 at 0.05 microgram/ml. This Fab also inhibited plaque formation when applied to virus-infected monolayers, completely abolishing HSV-2 plaque development at 25 micrograms/ml 72 hr postinfection, indicating the ability of the Fab to prevent cell-to-cell spread of virus. The Fab was shown to recognize viral glycoprotein D and to neutralize virus primarily by a postattachment mechanism. Recombinant Fabs may be useful for topical administration, although whole antibody will probably be required for systemic use.
BMS-936564/MDX-1338: A Fully Human Anti-CXCR4 Antibody Induces Apoptosis In Vitro and Shows Antitumor Activity In Vivo in Hematologic Malignancies (2012)

BMS-936564/MDX-1338 is a potent CXCR4 antagonist which is efficacious as monotherapy in tumor-bearing mice and is currently in phase I for the treatment of relapsed/refractory AML, NHL, CLL, and multiple myeloma.
Influence of Immunoadsorption on the Removal of Immunoglobulin G Autoantibodies in Crescentic Glomerulonephritis (1993)

We report the treatment of 5 patients with crescentic glomerulonephritis by immunoadsorption using a protein A column. Two had systemic vasculitis, 2 antiglomerular basement membrane disease and 1 systemic lupus erythematosus (SLE). In the patients with systemic vasculitis and SLE, there was successful removal of autoantibodies and rapid control of disease; remission was maintained over a mean follow-up of 2 years. Clinical improvement was not seen in 2 patients with anti-glomerular basement membrane (GBM) disease who presented with dialysis-dependent renal failure. There were no apparent clinical side-effects related to the immunoadsorption procedure. Protein A immunoadsorption offers a semiselective alternative to plasma exchange and appears to be safe and efficient in removing pathogenic autoantibodies in crescentic glomerulonephritis without anti-GBM antibodies.
A compiler scheme for reusing intermediate computation results (2004)

Recent research has shown that programs often exhibit value locality. Such locality occurs when a code segment, although executed repeatedly in the program, takes only a small number of different values as input and, naturally, generates a small number of different outputs. It is potentially beneficial to replace such a code segment by a table, which records the computation results for the previous inputs. When the program execution re-enters the code segment with a repeated input, its computation can be simplified to a table look-up. We discuss a compiler scheme to identify code segments, which are good candidates for computation reuse. We discuss the conditions under which the table look-up costs less than repeating the execution, and we perform profiling to identify candidates, which have many repeated inputs at run time. Compared to previous work, this scheme requires no special hardware support and is therefore particularly useful for resource constrained systems such as handheld computing devices. We implement our scheme and its supporting analyses in GCC. We experiment with several multimedia benchmarks and the GNU Go game by executing them on a handheld computing device. The results show the scheme to improve the performance and to reduce the energy consumption quite substantially for these programs.
Water purification by membranes: The role of polymer science (2010)

Abstract Two of the greatest challenges facing the 21st century involve providing sustainable supplies of clean water and energy, two highly interrelated resources, at affordable costs. Membrane technology is expected to continue to dominate the water purification technologies owing to its energy efficiency. However, there is a need for improved membranes that have higher flux, are more selective, are less prone to various types of fouling, and are more resistant to the chemical environment, especially chlorine, of these processes. This article summarizes the nature of the global water problem and reviews the state of the art of membrane technology. Existing deficiencies of current membranes and the opportunities to resolve them with innovative polymer chemistry and physics are identified. Extensive background is provided to help the reader understand the fundamental issues involved. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2010
Immunoglobulin superfamily proteins: Structure, mechanisms, and drug discovery (1997)

We review the recent progress made in our laboratories in structure-based drug design targeting proteins of the immunoglobulin superfamily (IgSF). We will focus on the CD4 protein, which is involved in T cell function, as a specific example of how the general concept and methodologies can be applied. Recent studies of CD4 structure and function have revealed new insight into possible mechanisms for CD4 self-association and its role in binding to major histocompatibility complex (MHC) class II molecules and initiation of T cell activation. This has led to the formulation of a hypothetical model of co-oligomerization of CD4, MHC class II, and T cell receptor (TCR). Such a basic understanding of CD4 structure and mechanisms has aided the development of a new generation of potential immunotherapeutics targeting specific CD4 surface functional sites. The design and discovery of small molecular inhibitors of CD4 and other IgSF proteins, in peptide, peptidomimetic, and nonpeptidic organic forms have opened new avenues for chemical research in which peptide, organic, and more recently combinatorial chemistry techniques can be used to further develop these promising lead analogs into a new generation of effective pharmaceuticals.
Pharmacokinetics of Wood Creosote: Glucuronic Acid and Sulfate Conjugation of Phenolic Compounds (1995)

Wood creosote, principally a mixture of non-, alkyl- and/or alkoxy-substituted phenolic compounds, was orally administered to adult male volunteers to determine its metabolites and pharmacokinetic parameters. After a 133-mg single dose, its major constituents (i.e. phenol 15 mg, guaiacol 32 mg, p-cresol 18 mg and creosol 24 mg) were found in peripheral venous blood and urine, mostly as glucuronic acid and, except for creosol, as sulfate conjugates. Low concentrations of unconjugated phenols were also detected. The metabolites in the serum started to increase 15 min after the dose, and they reached their maximum concentrations 30 min after administration. The maximum concentrations of glucuronides were 0.18 +/- 0.07, 0.91 +/- 0.38, 0.33 +/- 0.18 and 0.47 +/- 0.23 mg/l; those of sulfates were 0.16 +/- 0.06, 0.22 +/- 0.09, 0.17 +/- 0.07 and < 0.04 mg/l for phenol, guaiacol, p-cresol and creosol, respectively. The 24-hour urinary recoveries of the sum of each compound and its metabolites were 75 +/- 35, 45 +/- 36, 103 +/- 51 and 74 +/- 36%, in the above order. The presence of guaiacol glucuronide in blood and urine was directly verified by its isolation and structure analyses.
IL-7 comes of age (2006)

Kim and colleagues demonstrate that aging is associated with diminished numbers of IL-7Rα–expressing T cells and that these cells have decreased responsiveness to IL-7, with important implications for the clinical development of IL-7 as an immunomodulatory agent. 

Interleukin 7 (IL-7) is a
Simultaneous Runs of the Bayer VERSANT HIV-1 Version 3.0 and HCV bDNA Version 3.0 Quantitative Assays on the System 340 Platform Provide Reliable Quantitation and Improved Work Flow (2004)

Branched DNA (bDNA) assays to quantify human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) consist of three distinct steps, including sample processing, hybridization, and detection, and utilize the System 340 platform for plate incubation and washing. Sample processing differs: HIV-1 from 1 ml of plasma is concentrated by high-speed centrifugation, whereas HCV plasma or serum samples are used without concentration. The first step of hybridization involves viral lysis at 63 degrees C: HIV-1 is performed in a heat block, whereas HCV is performed in System 340. The remaining hybridization and detection steps are similar for HIV-1 and HCV and executed on System 340. In the present study, the HIV-1 bDNA assay was adapted for viral lysis in the System 340 platform. The adaptation, test method 2, includes a 20-s vortex of concentrated viral pellet and lysis working solution, transfer of viral lysate to the 96-well capture plate, and transfer to System 340 programmed for HCV assay specifications. With test method 2, specificity and quantification were within assay specifications. HCV bDNA methodology remains unchanged. Hence, an HIV-1 and an HCV bDNA can be run simultaneously on System 340. With simultaneous testing, laboratories can run full plates, as well as combinations of full and partial plates. Also, simultaneous HIV-1 and HCV bDNA permits labor consolidation and improved workflow while maintaining multitasking and rapid patient result turnaround.
Platelet-derived growth factor receptors form a high affinity state in membrane preparations. Kinetics and affinity cross-linking studies. (1984)

The specific binding of 125I-PDGF (platelet-derived growth factor) to intact fibroblasts becomes relatively nondissociable during incubation at 37 degrees C. To characterize the interaction of PDGF with its receptors under conditions in which there is no receptor internalization, we have studied the binding of 125I-PDGF to membrane preparations derived from mouse 3T3 cells and rat liver. The binding sites had the affinity and specificity characteristics expected of PDGF receptors. At 37 degrees C (but not at 4 degrees C) the specific binding of 125I-PDGF to membranes gradually became nondissociable as assessed by either dilution or by addition of excess unlabeled PDGF. This tight binding was not due to a covalent interaction since the polyanionic compound suramin readily dissociated specifically bound 125I-PDGF. This property of suramin was used to expose rat liver PDGF receptors which were occupied by endogenous PDGF. Affinity cross-linking studies demonstrated that the formation of the nondissociable state of 125I-PDGF binding was associated with the binding of 125I-PDGF to a 160,000-dalton protein and to a 110,000-dalton species. The cross-linked binding sites could be adsorbed to wheat germ agglutinin and to anion exchange resins. The isoelectric point of both cross-linked species determined by two-dimensional gel electrophoresis was approximately 4.7. These data demonstrate that in membrane preparations, PDGF binds to an anionic 160,000-dalton glycoprotein which is likely to be the receptor. A high affinity state of PDGF binding, which is formed rapidly at 37 degrees C, can be dissociated by suramin.
A Receptor/Cytoskeletal Movement Triggered by Costimulation During T Cell Activation (1998)

During T cell activation, the engagement of costimulatory molecules is often crucial to the development of an effective immune response, but the mechanism by which this is achieved is not known. Here, it is shown that beads attached to the surface of a T cell translocate toward the interface shortly after the start of T cell activation. This movement appears to depend on myosin motor proteins and requires the engagement of the major costimulatory receptor pairs, B7-CD28 and ICAM-1-LFA-1. This suggests that the engagement of costimulatory receptors triggers an active accumulation of molecules at the interface of the T cell and the antigen-presenting cell, which then increases the overall amplitude and duration of T cell signaling.
p38 Mitogen-Activated Protein Kinase-Dependent and -Independent Signaling of mRNA Stability of AU-Rich Element-Containing Transcripts (2002)

Adenylate/uridylate-rich element (ARE)-mediated mRNA turnover is an important regulatory component of gene expression for innate and specific immunity, in the hematopoietic system, in cellular growth regulation, and for many other cellular processes. This diversity is reflected in the distribution of AREs in the human genome, which we have established as a database of more than 900 ARE-containing genes that may utilize AREs as a means of controlling cellular mRNA levels. The p38 mitogen-activated protein kinase (MAP kinase) pathway has been implicated in regulating the stability of nine ARE-containing transcripts. Here we explored the entire spectrum of ARE-containing genes for p38-dependent regulation of ARE-mediated mRNA turnover with a custom cDNA array containing probes for 950 ARE mRNAs. The human monocytic cell line THP-1 treated with lipopolysaccharide (LPS) was used as a reproducible cellular model system that allowed us to precisely control the conditions of mRNA induction and decay in the absence and presence of the p38 inhibitor SB203580. This approach allowed us to establish an LPS-induced ARE mRNA expression profile in human monocytes and determine the half-lives of 470 AU-rich mRNAs. Most importantly, we identified 42 AU-rich genes, previously unrecognized, that show p38-dependent mRNA stabilization. In addition to a number of cytokines, several interesting novel AU-rich transcripts likely to play a role in macrophage activation by LPS exhibited p38-dependent transcript stabilization, including macrophage-specific colony-stimulating factor 1, carbonic anhydrase 2, Bcl2, Bcl2-like 2, and nuclear factor erythroid 2-like 2. Finally, the identification of the p38-dependent upstream activator MAP kinase kinase 6 as a member of this group identifies a positive feedback loop regulating macrophage signaling via p38 MAP kinase-dependent transcript stabilization.
Progress in Piezotronics and Piezo‐Phototronics (2012)

The fundamental principle of piezotronics and piezo-phototronics were introduced by Wang in 2007 and 2010, respectively. Due to the polarization of ions in a crystal that has non-central symmetry in materials such as the wurtzite structured ZnO, GaN and InN, a piezoelectric potential (piezopotential) is created in the crystal by applying a stress. Owing to the simultaneous possession of piezoelectricity and semiconductor properties, the piezopotential created in the crystal has a strong effect on the carrier transport at the interface/junction. Piezotronics is about the devices fabricated using the piezopotential as a "gate" voltage to tune/control charge carrier transport at a contact or junction. The piezo-phototronic effect is to use the piezopotential to control the carrier generation, transport, separation and/or recombination for improving the performance of optoelectronic devices, such as photon detector, solar cell and LED. This manuscript reviews the updated progress in the two new fields. A perspective is given about their potential applications in sensors, human-silicon technology interfacing, MEMS, nanorobotics and energy sciences.
Lectin-Mediated Bioadhesion: Preparation, Stability and Caco-2 Binding of Wheat Germ Agglutinin-Functionalized Poly(D,L-lactic-co-glycolic acid)-Microspheres (2000)

To take advantage of the cytoadhesive characteristics of Wheat germ agglutinin (WGA) for improved particulate drug delivery, the interaction between WGA-grafted poly(D,L-lactic-co-glycolic acid)-microspheres and Caco-2 monolayers was investigated using bovine serum albumin (BSA) or glycine coated microspheres as a control. Covalent immobilization of WGA by the carbodiimide/N-hydroxysuccinimide-method on 4 microm microspheres yielded a surface density of 9.67+/-1.21x10(6) molecules/particle, whereas 0.22+/-0.04x10(6) WGA-molecules were bound by physical adsorption. After storage for 21 days in HEPES-buffer and treatment of the particles with 5 M urea, 86% of covalently linked lectin was still attached to the particles. At 4 degrees C the Caco-2 binding rate of both, WGA- and BSA-modified particles increased with addition of increasing numbers of particles until saturation was reached at 38150+/-1740 (WGA) or 12066+/-1195 (BSA) microspheres bound/mm(2) Caco-2 monolayer. Inhibition of Caco-2 binding of WGA-functionalized microspheres by chitotriose indicated for specificity of the interaction. As observed by confocal laser scanning microscopy, the fluorescein-loading of the particles was accumulated intracellularly after incubation of Caco-2 monolayers with WGA-modified microspheres contrary to glycine-grafted microspheres. Additionally, in case of WGA-functionalized microspheres the amount of cell associated fluorescein was 200-fold higher than that of the free solution. In conclusion, WGA-modified microspheres are expected to enhance intestinal transport of incorporated drugs due to cytoadhesion provided by the lectin coating.
Regio- and Stereoselectivity of Particulate Methane Monooxygenase from Methylococcus capsulatus (Bath) (1997)

The regiospecificity and stereoselectivity of alkane hydroxylation and alkene epoxidation by the particulate methane monooxygenase from Methylococcus capsulatus (Bath) was evaluated over a range of substrates. Oxidation products were identified by conventional GC analysis, and the stereoselectivity of oxidation was determined by a combination of chiral GC and HPLC methods, as well as 1H NMR analysis of the corresponding (R)-2-acetoxy-2-phenylethanoate ester derivatives in the case of alkanol products. Alkane hydroxylation was found to proceed favoring attack at the C-2 position in all cases, and the stereoselectivity for n-butane and n-pentane was characterized by an enantiomeric excess of 46% and 80%, respectively, with preference for the (R)-alcohol noted for both substrates. Epoxides were formed with smaller stereoselectivities. Together, the regio- and stereoselectivity results suggest that an equilibrium of competing substrate binding modes exists. A simple substrate-binding model that incorporates preferential C-2 oxidation with the observed stereoselectivity of alkane hydroxylation is proposed, and hypotheses for the general mechanism are suggested and discussed.