gebhart/patrepeval huggingface dataset:
VLA‐3: A novel polypeptide association within the VLA molecular complex: cell distribution and biochemical characterization (1986)

The family of human T cell activation-associated proteins, named VLA complex, is formed by the molecular association of cell surface glycoproteins of 210, 165, 130 and 80 kDa. In this report, we describe eight different monoclonal antibodies (HP mAb) specific for the 80-kDa polypeptide which preferentially associates with the 165-kDa member. Comparative immunoprecipitation and cell-binding studies demonstrated that the HP mAb recognize an epitope(s) on the 165/80 kDa subset different from those recognized by other anti-VLA mAb previously described. Furthermore, cellular and tissue distribution studies by flow cytometry and peroxidase staining showed that the HP reactivity pattern is different from other VLA specificities. The 165/80-kDa complex defined by HP mAb is present on human thymocytes, peripheral blood lymphocytes as well as on T, B and myelomonocytic cell lines. However, only the 80-kDa subunit was precipitated by HP mAb from activated T lymphocytes. These results suggest that the association between the 165- and 80-kDa subunits diminishes during the activation process, and that the epitopes recognized by the HP mAb are located on the 80-kDa protein. The novel polypeptide association of 165/80 kDa has been termed VLA-3.
Benzimidazole condensed ring systems. 1. Syntheses and biological investigations of some substituted pyrido[1,2‐a]benzimidazoles (1988)

Abstract The synthesis of some substituted 3‐hydroxy‐1‐oxo‐1 H,5H ‐pyrido[1,2‐ a ]benzimidazole‐4‐carbonitriles and 4‐ethyl carboxylates 3 and their 0‐ and N ‐dialkyl derivatives 5,6 is described. 3‐Ethoxy‐5‐ethyl‐2‐phenyl‐1 H,5H ‐pyrido[1,2‐ a ]benzimidazol‐1‐one 7 was obtained during the course of ethylating the parent ester 3t with triethyl phosphate. Chlorination of 3 with phosphorus oxychloride afforded the corresponding 1,3‐dichloropyrido[1,2‐ a ]benzimidazoles 8 which were converted to a variety of azido, amino, morpholino and methoxy derivatives of the system. The synthesis of the indolopyridobenzimidazole 15 is also described. Two compounds exhibited in vitro antibacterial activity. Many compounds were screened for antileukemic, antimicrobial, herbicidal and plant antifungal potencies but were inactive.
Regulation of tumor cell motility and migration by CD63 in a human melanoma cell line (1997)

CD63 belongs to the transmembrane 4 superfamily of membrane proteins and is expressed in several normal tissues as well as in melanoma cells. Previous reports have suggested that CD63 may play an important role in inhibiting melanoma progression, and this was supported by our studies showing that CD63 was associated with suppression of the growth of melanoma in nude mice. Recently, we and others have shown that CD63 may form noncovalent associations with beta1 integrins, which suggests that the function of CD63 may be related to that of integrins. To further explore the role of CD63 in melanoma, we transfected CD63 into a highly motile, CD63-negative melanoma cell line, KM3, which was shown to express alpha(v)beta5 as the predominant integrin with only trace amounts of beta1 integrins. Following transfection, CD63 was shown to associate with beta1 integrins, and beta1 expression appeared to be up-regulated. Cell motility in serum-containing media was markedly suppressed following transfection of CD63. This inhibition was potentiated by mAbs to CD63, and correlated with the level of CD63 expression. The CD63-transfected, but not the untransfected, melanoma cells showed increased adhesion and migration on the beta1 substrates, fibronectin, laminin, and collagen, whereas rates of migration were similar on the beta5 substrate, vitronectin. These results show that CD63 is involved in regulation of the motility of melanoma cells and their adhesion and migration on substrates associated with beta1 integrins. We suggest they provide further insights into the role of CD63 in tumor progression.
A comparison of two different assays for determining S-100B in serum and urine (2008)

The Sangtec and Elecsys assays are not interchangeable methods when analyzing S-100B in serum or urine samples after head injury.
Nutritional benefits of soy protein and soy fiber. (1991)

Soy protein and soy fiber are common ingredients in many foodstuffs. Various kinds of soy protein, including soy flour, soy-protein concentrate, and isolated soy protein, are currently used in human foods. Soy proteins are used in infant formulas and enteral nutrition products, as ingredients in meat products, and as protein supplements. Although it is a plant protein, the protein quality of soy protein is excellent. Soy fiber is used in enteral nutrition products and some bakery goods. Research shows that soy fiber provides the important health benefits usually associated with dietary fiber, including improved laxation and cholesterol-lowering ability. This review provides background information on soy protein and soy fiber and their use in human foods.
Overview of the lattice Boltzmann method for nano- and microscale fluid dynamics in materials science and engineering (2004)

The article gives an overview of the lattice Boltzmann method as a powerful technique for the simulation of single and multi-phase flows in complex geometries. Owing to its excellent numerical stability and constitutive versatility it can play an essential role as a simulation tool for understanding advanced materials and processes. Unlike conventional Navier–Stokes solvers, lattice Boltzmann methods consider flows to be composed of a collection of pseudo-particles that are represented by a velocity distribution function. These fluid portions reside and interact on the nodes of a grid. System dynamics and complexity emerge by the repeated application of local rules for the motion, collision and redistribution of these coarse-grained droplets. The lattice Boltzmann method, therefore, is an ideal approach for mesoscale and scale-bridging simulations. It is capable to tackling particularly those problems which are ubiquitous characteristics of flows in the world of materials science and engineering, namely, flows under complicated geometrical boundary conditions, multi-scale flow phenomena, phase transformation in flows, complex solid–liquid interfaces, surface reactions in fluids, liquid–solid flows of colloidal suspensions and turbulence. Since the basic structure of the method is that of a synchronous automaton it is also an ideal platform for realizing combinations with related simulation techniques such as cellular automata or Potts models for crystal growth in a fluid or gas environment. This overview consists of two parts. The first one reviews the philosophy and the formal concepts behind the lattice Boltzmann approach and presents also related pseudo-particle approaches. The second one gives concrete examples in the area of computational materials science and process engineering, such as the prediction of lubrication dynamics in metal forming, dendritic crystal growth under the influence of fluid convection, simulation of metal foam processing, flow percolation in confined geometries, liquid crystal hydrodynamics and processing of polymer blends.
Automatic Algorithm Selection in Computational Software Using Machine Learning (2016)

Computational software programs, such as Maple and Mathematica, heavily rely on superfunctions and meta-algorithms to select the optimal algorithm for a given task. These meta-algorithms may require intensive mathematical proof to formulate, incur large computational overhead, or fail to consistently select the best algorithm. Machine learning demonstrates a promising alternative for automatic algorithm selection by easing the design process and overhead while also attaining high accuracy in selection. In a case study on the resultant superfunction, a trained neural network is able to select the best algorithm out of the four available 86% of the time in Maple and 78% of the time in Mathematica. When used as a replacement for pre-existing meta-algorithms, the neural network brings about a 68% runtime improvement in Maple and 49% improvement in Mathematica. Random forests, k-nearest neighbors, and both linear and RBF kernel SVMs are also compared to the neural network model, the latter of which offers the best performance out of the tested machine learning methods.
Gene cloning and expression in lactic streptococci (1987)

Recent developments have made the mesophilic lactic streptococci, widely used in dairy fermentations, accessible to genetic manipulation. Several host-vector systems have been described which currently are used in the cloning and expression of homologous and heterologous genes. The essential elements of these systems, the various cloning strategies and the first successful cloning experiments are described with emphasis on the molecular organization of proteinase genes. In addition, the organization and nucleotide sequence of signals which are involved in gene expression in lactic streptococci are summarized.
Tightly regulated and inducible expression of a yoked hormone-receptor complex in HEK 293 cells (2004)

We have previously reported the construction of a constitutively active luteinizing hormone receptor by covalently linking a fused heterodimeric hormone to the extracellular domain of the G protein-coupled receptor. This yoked hormone-receptor complex (YHR) was found to produce high levels of cAMP in the absence of exogenous hormone. Stable lines expressing YHR were generated in HEK 293 cells to obtain lines with different expression levels; however, in a relatively short time of continued passage, it was found that YHR expression was greatly reduced. Herein, we describe the development of clonal lines of HEK 293 cells in which the expression of YHR is under the control of a tetracycline-regulated system. Characterization of clonal lines revealed tight control of YHR expression both by dose and time of incubation with doxycycline. These experiments demonstrated a good correlation between expression levels of the receptor and basal cAMP production. Moreover, the reduction in receptor expression following doxycycline removal revealed that YHR mRNA and protein decayed at similar rates, again suggesting a strong linkage between mRNA and protein levels. The controlled expression of YHR in this cell system will allow for a more detailed analysis of the signaling properties associated with constitutive receptor activation and may prove to be advantageous in developmental studies with transgenic animals.
The Putative Nucleocapsid and Envelope Protein Genes of Hepatitis C Virus Determined by Comparison of the Nucleotide Sequences of Two Isolates Derived from an Experimentally Infected Chimpanzee and Healthy Human Carriers (1990)

cDNA fragments of a 5'-terminal region of the hepatitis C virus (HCV) genome were isolated by the reverse polymerase chain reaction from RNA extracted from plasma samples of healthy Japanese carriers. Their nucleotide sequence was compared with that of the original isolate which had been passaged twice in chimpanzees. No deletions or insertions were observed between the two sequences in the regions examined. Both the 5' untranslated and putative nucleocapsid (core) protein regions were highly conserved (99% and 91% nucleotide identities, respectively). In contrast, the region immediately downstream which encodes a putative envelope glycoprotein(s) showed only 74% nucleotide identity between the two isolates. At the polypeptide level, the core and envelope domains showed 97% and 75% amino acid identities, respectively. This envelope variation may reflect the adaptation of HCV to the different hosts and/or the result of immunological selection. The highly conserved nucleotide sequence of the 5' untranslated and core regions may play an important regulatory role in the life cycle of HCV.
Sustained alpha‐sarcoglycan gene expression after gene transfer in limb‐girdle muscular dystrophy, type 2D (2010)

The findings of this gene replacement study in LGMD2D subjects have important implications not previously demonstrated in muscular dystrophy. Long-term, sustainable gene expression of alpha-sarcoglycan was observed following gene transfer mediated by AAV. The merit of a muscle-specific tMCK promoter, not previously used in a clinical trial, was evident, and the potential for reversal of disease was displayed.
Mobile agent security and Telescript (2002)

Telescript is a software technology for building distributed applications using the mobile agent paradigm. Telescript mobile agents are migrating processes capable of being executed on any Telescript service host. Currently, Telescript incorporates safety and security features sufficient for deploying the first generation of mobile agent applications, subject to certain operating restrictions. The ultimate goal is the safe hosting of arbitrary, previously unseen programs, or "programming the network".
Inhibition of gap junction and adherens junction assembly by connexin and A-CAM antibodies. (1992)

We examined the roles of the extracellular domains of a gap junction protein and a cell adhesion molecule in gap junction and adherens junction formation by altering cell interactions with antibody Fab fragments. Using immunoblotting and immunocytochemistry we demonstrated that Novikoff cells contained the gap junction protein, connexin43 (Cx43), and the cell adhesion molecule, A-CAM (N-cadherin). Cells were dissociated in EDTA, allowed to recover, and reaggregated for 60 min in media containing Fab fragments prepared from a number of antibodies. We observed no cell-cell dye transfer 4 min after microinjection in 90% of the cell pairs treated with Fab fragments of antibodies for the first or second extracellular domain of Cx43, the second extracellular domain of connexin32 (Cx32) or A-CAM. Cell-cell dye transfer was detected within 30 s in cell pairs treated with control Fab fragments (pre-immune serum, antibodies to the rat major histocompatibility complex or the amino or carboxyl termii of Cx43). We observed no gap junctions by freeze-fracture EM and no adherens junctions by thin section EM between cells treated with the Fab fragments that blocked cell-cell dye transfer. Gap junctions were found on approximately 50% of the cells in control samples using freeze-fracture EM. We demonstrated with reaggregated Novikoff cells that: (a) functional interactions of the extracellular domains of the connexins were necessary for the formation of gap junction channels; (b) cell interactions mediated by A-CAM were required for gap junction assembly; and (c) Fab fragments of antibodies for A-CAM or connexin extracellular domains blocked adherens junction formation.
Multiple Functions of Glutamate Uptake via Meningococcal GltT-GltM l -Glutamate ABC Transporter in Neisseria meningitidis Internalization into Human Brain Microvascular Endothelial Cells (2015)

We previously reported that Neisseria meningitidis internalization into human brain microvasocular endothelial cells (HBMEC) was triggered by the influx of extracellular L-glutamate via the GltT-GltM L-glutamate ABC transporter, but the underlying mechanism remained unclear. We found that the ΔgltT ΔgltM invasion defect in assay medium (AM) was alleviated in AM without 10% fetal bovine serum (FBS) [AM(-S)]. The alleviation disappeared again in AM(-S) supplemented with 500 μM glutamate. Glutamate uptake by the ΔgltT ΔgltM mutant was less efficient than that by the wild-type strain, but only upon HBMEC infection. We also observed that both GltT-GltM-dependent invasion and accumulation of ezrin, a key membrane-cytoskeleton linker, were more pronounced when N. meningitidis formed larger colonies on HBMEC under physiological glutamate conditions. These results suggested that GltT-GltM-dependent meningococcal internalization into HBMEC might be induced by the reduced environmental glutamate concentration upon infection. Furthermore, we found that the amount of glutathione within the ΔgltT ΔgltM mutant was much lower than that within the wild-type N. meningitidis strain only upon HBMEC infection and was correlated with intracellular survival. Considering that the L-glutamate obtained via GltT-GltM is utilized as a nutrient in host cells, l-glutamate uptake via GltT-GltM plays multiple roles in N. meningitidis internalization into HBMEC.
A focused antibody library for improved hapten recognition (2005)

The topography of the antigen-binding site as well as the number and the positioning of the antigen contact residues are strongly correlated with the size of the antigen with which the antibody interacts. On the basis of these considerations, we have designed a focused scFv repertoire biased for haptens, designated the cavity library. The hapten-specific scFv, FITC8, was used as a scaffold for library construction. FITC8, like other hapten binders, displays a characteristic cavity in its paratope into which the hapten binds. In five of the six complementarity-determining regions, diversity-carrying residues were selected rationally on the basis of a model structure of FITC8 and on known antibody structure-function relationships, resulting in variation of 11 centrally located, cavity-lining residues. L3 was allowed to carry a more complex type of diversity. In addition, length variation was introduced into H2, as longer versions of this loop have been shown to correlate with increased hapten binding. The library was screened, using phage display, against a panel of five different haptens, yielding diverse and highly specific binders to four of the antigens. Parallel selections were performed with a library having diversity spread onto a greater area, including more peripherally located residues. This resulted in the isolation of binders, which, in contrast to the clones selected from the cavity library, were not able to bind to the soluble hapten in the absence of the carrier protein. Thus, we have shown that by focusing diversity to the hotspots of interaction a library with improved hapten-binding ability can be created. The study supports the notion that it is possible to create antibody libraries that are biased for the recognition of antigens of pre-defined size.
The Study of Quality of Service in Object-based Storage Device (2006)

Object-based storage(OBS),considered as the next Internet storage protocol standard,has been accepting gradually.Object-based storage device(OSD)can give more support on applications' Quality of Service(QoS)require- ments.This paper firstly analyses object-based storage system's QoS requirements,discusses how to translate QoS re- quirements to QoS attributes and extends the OSD SCSI protocol standard to support QoS,then using quantify analysis method,analyses QoS and the process of communicating QoS information between application and OSD.finally,in- tegrating the OSD's characters,the paper proposes a QoS three-layer model called Q-Model and an optimization arith- metic called BRP in OSD.
Performance Assessment of Noise-Suppressed Nyquist-WDM for Terabit Superchannel Transmission (2012)

This paper focuses on terabit superchannel transmission with enhanced network reach by using an emerging noise-suppressed Nyquist wavelength division multiplexing (NS-N-WDM) technique for polarization multiplexing quadrature phase shift keying subchannels at different symbol rate to subchannel spacing ratios up to 1.28, and for the first time, it was compared experimentally with the transmission capability of no-guard-interval coherent optical orthogonal frequency division multiplexing (NGI-CO-OFDM) on the same testbed. At 2 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> bit error ratio, the maximum reachable distance is 3200 and 2800 km SMF-28 with erbium-doped-fiber-amplifier-only amplification for NGI-CO-OFDM and NS-N-WDM terabit superchannels, respectively, at 100 Gb/s/ch. For 11 × 112 and 11 × 128 Gb/s/ch NS-N-WDM transmission under assumption of different coding gain with hard-decision and soft-decision forward error correction, their maximum achievable distance was found to be equivalent, which are 2100 and 2170 km, respectively, both were achieved by using digital noise filtering and 1-bit maximum likelihood sequence estimation at the receiver DSP. In addition, the back-to-back characteristics of NS-N-WDM superchannel such as analog-to-digital converter bandwidth requirement and its tolerance to unequal subchannel power were experimentally evaluated and studied.
Solution Structure and Dynamics of the Plasminogen Kringle 2−AMCHA Complex:  31-Helix in Homologous Domains, (1999)

The kringle 2 (K2) module of human plasminogen (Pgn) binds L-lysine and analogous zwitterionic compounds, such as the antifibronolytic agent trans-(aminomethyl)cyclohexanecarboxylic acid (AMCHA). Far-UV CD and NMR spectra reveal little conformational change in K2 upon ligand binding. However, retarded (1)H-(2)H isotope exchange kinetics induced by AMCHA indicate stabilization of the K2 conformation by the ligand. Assessment of secondary structure content from CD spectra yields approximately 26% beta-STRAND, approximately 13% beta-TURN, approximately 15% 3(1)-HELIX, and approximately 6% 3(10)-HELIX. The NMR solution conformation of the K2 domain complexed to AMCHA has been determined [heavy atom rmsd = 0.49 +/- 0.09A (BACKBONE) AND 1.02+/- 0.08 (ALL)]. The K2 molecule has overall dimensions of approximately 34.5A times approximately 33.4A times approximately 22.7A . Analogous with the polypeptide outline of homologous domains, K2 contains three short antiparallel beta-sheets (paired strands 15-16/20-21, 24-25/48-49, and 62-64/72-74) and four defined beta-turns (residues 6-9, 16-19, 53-56, AND 67-70). Consistent with the CD analysis, albeit novel in the context of kringle folding, the NMR structure reveals an unpaired beta-strand structured by residues 30-32, a turn of 3(10)-helix compromising residues 38-41, and a 3(1)-helix for residues 21-24 and 74-79. We also identify alignable 3(1)-helices in previously reported homologous kringle structures. Rather high order parameter S(2) values (<S(2)>= approximately 0.85 +/- 0.04) characterize the K2 backbone dynamics. The lowest flexibility is observed for the two inner loop segments of residues 51-63 AND 63-75 (<S(2)>= approximately 0.86-0.87 +/- 0.03). Overhauser connectivities reveal close hydrophobic contacts of the ligand ring with side chains of Tyr(36), Trp(62), Phe(64), Trp(72), AND Leu(74). In most K2 structures, the N atom of AMCHA places itself approximately 3.9 and 4.4A from the anionic groups of Glu(57) and Asp(55), respectively, while its carboxylate group, H-bonded to the Tyr(36) side chain OH(eta), ion-pairs the Arg(71) guanidinium group. Consistent with the preference of K2 for binding 5-aminopentanoic acid over 6-aminohexanoic acid, the positions of the ionic centers within the K2 binding site approach each other approximately 1A closer relative to what is observed in lysine binding sites of homologous Pgn modules.
Gene silencing in mammalian cells by PCR‐based short hairpin RNA (2003)

RNA interference (RNAi) provides a powerful tool to silence genes in a sequence-specific manner in a variety of systems. However, not all sequences are effective in the RNAi-mediated gene silencing. In this study, we developed a polymerase chain reaction (PCR)-based RNAi strategy for a quick screening of small interfering RNA (siRNA) efficiency. This method utilized a two-step PCR to generate a chimeric DNA template containing the U6 promoter or cytomegalovirus promoter and short hairpin DNA. We demonstrated that the transfection of the PCR products into mammalian cells resulted in specific depressions of exogenous (luciferase, green fluorescent protein and beta-galactosidase) and endogenous (annexin II) gene expressions. This PCR strategy provides a rapid, easy and cheap approach for testing candidates siRNA sequences and is an attractive alternative to subcloning.