gebhart/patrepeval huggingface dataset:
High-voltage electroporation of bacteria: genetic transformation of Campylobacter jejuni with plasmid DNA. (1988)

Electroporation permits the uptake of DNA by mammalian cells and plant protoplasts because it induces transient permeability of the cell membrane. We investigated the utility of high-voltage electroporation as a method for genetic transformation of intact bacterial cells by using the enteric pathogen Campylobacter jejuni as a model system. This report demonstrates that the application of high-voltage discharges to bacterial cells permits genetic transformation. Our method involves exposure of a Campylobacter cell suspension to a high-voltage exponential decay discharge (5-13 kV/cm) for a brief period of time (resistance-capacitance time constant = 2.4-26 msec) in the presence of plasmid DNA. Electrical transformation of C. jejuni results in frequencies as high as 1.2 x 10(6) transformants per microgram of DNA. We have investigated the effects of pulse amplitude and duration, cell growth conditions, divalent cations, and DNA concentration on the efficiency of transformation. Transformants of C. jejuni obtained by electroporation contained structurally intact plasmid molecules. In addition, evidence is presented that indicates that C. jejuni possesses DNA restriction and modification systems. The use of electroporation as a method for transforming other bacterial species and guidelines for its implementation are also discussed.
Understanding unsegmented user utterances in real-time spoken dialogue systems (1999)

This paper proposes a method for incrementally understanding user utterances whose semantic boundaries are not known and responding in real time even before boundaries are determined. It is an integrated parsing and discourse processing method that updates the partial result of understanding word by word, enabling responses based on the partial result. This method incrementally finds plausible sequences of utterances that play crucial roles in the task execution of dialogues, and utilizes beam search to deal with the ambiguity of boundaries as well as syntactic and semantic ambiguities. The results of a preliminary experiment demonstrate that this method understands user utterances better than an understanding method that assumes pauses to be semantic boundaries.
The Structural Requirements of Epitopes with Ige Binding Capacity Demonstrated by Three Major Allergens from Fish, Egg and Tree Pollen (1991)

Three major allergens from cod fish, egg white and tree pollen, were characterized by studies on their allergenic and antigenic structures. The major allergen of cod fish, Allergen M "parvalbumins pI 4.75", is composed of 113 amino acid residues with a molecular weight of 12,328 daltons. It comprised three domains, AB, CD and EF, consisting of 3 helices interspaced by one loop. Each of the loops of the CD and EF domains each coordinates one Ca2+. The antigenicity and allergenicity of Allergen M was deduced from studying the modified protein and some particular synthetic peptides. Three sites were encompassing IgE binding epitopes namely peptides 33-44, 65-74 and 88-96. A novel peptide (49-64), of the CD-domain, was demonstrated to be allergenically/antigenically active and cross reactive with birch pollen allergen, which incidentally was used as a negative control. This site encompassed two repetitive sequences (D-E-D-K) and (D-E-L-K), suggested to be mutually critical for the specificity of antibody binding. This hypothesis was reconfirmed by SPPS of several analogous peptides of region 39-64. Furthermore, peptide 88-103 of the EF-domain was similarly synthesized; it functioned as a monovalent hapten, blocking and not eliciting allergic reaction. Moreover, peptide 13-32 of domain AB, the non-calcium binding domain, was thoroughly tested. The results of PK inhibition showed clear activity and the peptide was found to function at the level of a divalent determinant. Ovalbumin (OA) is the most dominant of five major allergens of egg white and universally used as model protein. OA allergenic epitopes were shown to be mainly determined by the primary structure and depend on certain peptide chain length. The N-terminal decapeptide (OA 1-10) was shown to react with reaginic IgE. Direct skin test on egg allergic patients, showed no activity and the site was therefore concluded to encompasses one single Ig binding haptenic epitope. Peptide OA 323-339, was demonstrated to be valuable in studies of T-cell recognition of protein antigens. Three analogous peptides of this region were prepared and clearly shown to be immunogenic in rabbits and to bind specific IgE from patients allergic to egg. OA 323-339 was concluded to encompass an allergenic and antigenic epitope which was recognized by human and rabbit B-lymphocytes. Eight peptides in the region 11-122 were similarly synthesized. A test battery was performed to study this region using rabbit polyclonal antibodies and human specific IgE. Some of these sites were involved in binding of particular Ig paratopes. Five immunogenic peptides from the major allergens of tree pollen extracts (segment 23-38), were synthesized. The selection of those peptides was setteled using two algorithms for providing the optimal hydrophobicity.(ABSTRACT TRUNCATED AT 400 WORDS)
Some Problems in Analysis and Design of Thin/Thick Plate (2005)

There are some interesting problems and pitfalls in plate analysis and design which are worth reviewing. The applications of boundary conditions, stress recovery, support stiffness, lateral shear force and design of shear are addressed in the paper. It is recommended that greater care must be paid if a proper analysis is to be performed, and cost saving may be possible in some situations.
Site-directed mutageneses of rat liver cytochrome P-450d: axial ligand and heme incorporation (1988)

By oligonucleotide-directed mutageneses, 13 substitutions of amino acids at the carboxy-terminal region of rat liver cytochrome P-450d were done as follows: (A) Phe-449----Tyr; (B) Gly-450----Ser; (C) Leu-451----Ser; (D) Gly-452----Glu; (E) Lys-453----Glu; (F) Arg-454----Leu; (G) Arg-455----Gly; (H) Cys-456----Tyr; (I) Cys-456----His; (J) Ile-457----Ser; (K) Gly-458----Glu; (L) Glu-459----Ala; (M) Ile-460----Ser. The CO-bound reduced forms of the wild type and mutants B-G, J, L, and M gave Soret peaks at 448 nm. The CO complex of mutant A gave a Soret peak at 445 nm. The intensities of the CO-bound forms of mutants A, C, D, and J were very small compared with that of the wild-type complex. The CO-reduced forms of mutants H, I, and K did not give a Soret peak around 450 nm at all. The 448-nm peak of mutant F was unstable and quickly disappeared with the concomitant appearance of a peak at 420 nm.(ABSTRACT TRUNCATED AT 250 WORDS)
SIMS 500 - Rapid Low Energy Secondary Ion Mass Spectrometer for In-Line Analysis of Gaseous Compounds - Technology and Applications in Automotive Emission Testing (1993)

&lt;div class="htmlview paragraph"&gt;A new multichannel gas analyzer based on ion - neutral interaction principles is introduced. This gas phase secondary ion mass spectrometer using several well defined energy levels for the ionization process quantitatively analyzes gas mixtures without the use of presetection techniques.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A high sensitivity for many compounds together with high cycle rates allows dynamic studies of gaseous emission in the low and sub ppm range.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Transient studies of inorganic compounds like NO, NH&lt;sub&gt;3&lt;/sub&gt;, H&lt;sub&gt;2&lt;/sub&gt;S, COS and SO&lt;sub&gt;2&lt;/sub&gt; in catalytic converter systems and differentiated Hydrocarbon analyses of C&lt;sub&gt;1&lt;/sub&gt; to C&lt;sub&gt;8&lt;/sub&gt; prove the versatility of the instrument.&lt;/div&gt;
Buffer insertion with adaptive blockage avoidance (2003)

Buffer insertion is a fundamental technology for very large scale integration interconnect optimization. This work presents the repeater insertion with adaptive tree adjustment (RIATA) heuristic that directly extends van Ginneken's classic algorithm to handle blockages in the layout. Given a Steiner tree containing a Steiner point that overlaps a blockage, a local adjustment is made to the tree topology that enables additional buffer insertion candidates to be considered. This adjustment adapts to the demand on buffer insertion and is incurred only when it facilitates the maximal slack solution. RIATA can be combined with any performance-driven Steiner tree algorithm and permits various solution search schemes to achieve different solution quality and runtime tradeoffs. Experiments on several large nets confirms that high-quality solutions can be obtained through this technique with greater efficiency than simultaneous approaches.
Direct observation of a DNA quadruplex by electrospray ionization mass spectrometry (1993)

In 10 mM sodium phosphate, pH 7.6, containing 0.1 mM ethylenediaminetetraacetic acid, ions correspondings to the non-calent, four-stranded oligonucleotide, d(CGCG4GCG)4, were detected by negative ion electrospray ionization (ESI) mass spectrometry at a low nozzle-skimmer (delta NS) bias (-150 V), but not at a higher delta NS bias (> -250 V). In contrast, when the sample was desalted and analyzed by ESI mass spectrometry at a low delta NS bias only ions for the single-stranded d(CGCG4GCG) species were observed. These data agree with spectroscopic evidence which showed that oligonucleotides with the sequence motif 5'd(CGCGnGCG)3', where n = 2-5, formed stable four-stranded complexes in the presence of monatomic cations, like K+, Ca2+, Na+ and Li+, but not in their absence.
SoftCel - an application of raster scan graphics to conventional cel animation (1979)

The system described uses frame buffers to provide digital analogues to the traditional processes of copying pencil drawings onto cels, painting them, and photographing them. The copying process is replaced by scanning the pencil drawings with a television camera and digitizing the video signal. Several image processing operations are performed on the digitized drawings to condition them for the next step, interactive painting of the drawings mediated by a computer program. The painted drawings are then combined with each other and painted backgrounds for frame by frame recording on film or video tape.
Stepwise Development of Hematopoietic Stem Cells from Embryonic Stem Cells (2009)

The cellular ontogeny of hematopoietic stem cells (HSCs) remains poorly understood because their isolation from and their identification in early developing small embryos are difficult. We attempted to dissect early developmental stages of HSCs using an in vitro mouse embryonic stem cell (ESC) differentiation system combined with inducible HOXB4 expression. Here we report the identification of pre-HSCs and an embryonic type of HSCs (embryonic HSCs) as intermediate cells between ESCs and HSCs. Both pre-HSCs and embryonic HSCs were isolated by their c-Kit(+)CD41(+)CD45(-) phenotype. Pre-HSCs did not engraft in irradiated adult mice. After co-culture with OP9 stromal cells and conditional expression of HOXB4, pre-HSCs gave rise to embryonic HSCs capable of engraftment and long-term reconstitution in irradiated adult mice. Blast colony assays revealed that most hemangioblast activity was detected apart from the pre-HSC population, implying the early divergence of pre-HSCs from hemangioblasts. Gene expression profiling suggests that a particular set of transcripts closely associated with adult HSCs is involved in the transition of pre-HSC to embryonic HSCs. We propose an HSC developmental model in which pre-HSCs and embryonic HSCs sequentially give rise to adult types of HSCs in a stepwise manner.
Steroid Hormone Metabolites Are Barbiturate-Like Modulators of the GABA Receptor (1986)

Two metabolites of the steroid hormones progesterone and deoxycorticosterone, 3 alpha-hydroxy-5 alpha-dihydroprogesterone and 3 alpha, 5 alpha-tetrahydrodeoxycorticosterone, are potent barbiturate-like ligands of the gamma-aminobutyric acid (GABA) receptor-chloride ion channel complex. At concentrations between 10(-7) and 10(-5)M both steroids inhibited binding of the convulsant t-butylbicyclophosphorothionate to the GABA-receptor complex and increased the binding of the benzodiazepine flunitrazepam; they also stimulated chloride uptake (as measured by uptake of 36Cl-) into isolated brain vesicles, and potentiated the inhibitory actions of GABA in cultured rat hippocampal and spinal cord neurons. These data may explain the ability of certain steroid hormones to rapidly alter neuronal excitability and may provide a mechanism for the anesthetic and hypnotic actions of naturally occurring and synthetic anesthetic steroids.
Inhibition of the Top-of-the-Line Corrosion under Stratified Flow (2001)

Abstract A new method is reported to protect carbon steel pipelines for wet transport of sweet and sour gases from internal corrosion up to the top-of-the line (TOL) by using corrosion inhibitors. The method functions not only at turbulent gas flow but also at stratified flow and even under stagnant conditions. According to the TOL spreading inhibitor concept inhibitor molecules are transported with a spreading liquid film (produced by spreading-active compounds) against the gravity from the bottom-of-the-line (BOL) along the pipe wall to the TOL. The paper describes the universal applicability of this concept which works under all surface conditions encountered in sweet or sour wet gas transport lines. The surface can be metallic clean, covered with mill scale, rust or corrosion product scales. These surfaces can be dry, water wet or hydrophobic. Careful tuning of the spreading system, composed of the 1- or 2-phase BOL liquid, the spreading agent and the corrosion inhibitor, yields optimum corrosion protection on the entire pipeline surface also at high water condensation rates.
Immobilization of Amine-Modified Oligonucleotides on Aldehyde-Terminated Alkanethiol Monolayers on Gold (2004)

Chemistry is described for the fabrication of DNA arrays on gold surfaces. Alkanethiols modified with terminal aldehyde groups are used to prepare a self-assembled monolayer (SAM). The aldehyde groups of the monolayer may be reacted with amine-modified oligonucleotides or other amine-bearing biomolecules to form a Schiff base, which may then be reduced to a stable secondary amine by treatment with sodium cyanoborohydride. The surface modifications and reactions are characterized by polarization modulation Fourier transform infrared reflection absorption spectroscopy (PM-FTIRRAS), and the accessibility, binding specificity, and stability of the DNA-modified surfaces are demonstrated in hybridization experiments.
Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase in a quaternary complex with a magnesium ion, NADPH and the antimalarial drug fosmidomycin (2007)

The crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) from Escherichia coli complexed with Mg(2+), NADPH and fosmidomycin was solved at 2.2 A resolution. DXR is the key enzyme in the 2-C-methyl-D-erythritol 4-phosphate pathway and is an effective target of antimalarial drugs such as fosmidomycin. In the crystal structure, electron density for the flexible loop covering the active site was clearly observed, indicating the well ordered conformation of DXR upon substrate binding. On the other hand, no electron density was observed for the nicotinamide-ribose portion of NADPH and the position of Asp149 anchoring Mg(2+) was shifted by NADPH in the active site.
Diagnostica-a Bayesian decision-aid system-applied to hypertension diagnosis (1993)

"Diagnostica" is a Bayesian statistical tool designed to collect and store the patient's data, suggest a diagnosis, and explain the decision in terms of density distributions. The program is written in C language on MacIntosh support. It is described using the case study of differential diagnosis between essential and secondary hypertensions (i.e., fibrodysplastic renal artery stenosis, atheromatous renal artery stenosis, Conn's syndrome, nephropathy and pheochromocytoma). Seventeen experimental parameters were taken into consideration, all of them available during the first medical examination. The density distributions of all items were established from the ARTEMIS experimental database. Both a priori probabilities of different types of hypertension and loss coefficients are taken into account in the calculations. Diagnostica can be used in a "make diagnosis" mode or in an "edition" mode. In the first case it can serve a physician in everyday practice; in the second it becomes a tool for medical research.
Mannose-Binding Lectin Recognizes Peptidoglycan via the N -Acetyl Glucosamine Moiety, and Inhibits Ligand-Induced Proinflammatory Effect and Promotes Chemokine Production by Macrophages (2005)

Peptidoglycan (PGN) is the major cell wall component (90%, w/w) of Gram-positive bacteria and consists of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) disaccharide repeating arrays that are cross-linked by short peptides. We hypothesized that PGN is a ligand for pathogen-associated pattern-recognition proteins. Mannose-binding lectin (MBL) and serum amyloid component P are two carbohydrate-binding innate immune proteins present in the blood. In this study we show that human MBL, but not serum amyloid component P, binds significantly to PGN via its C-type lectin domains, and that the interaction can be more effectively competed by GlcNAc than by MurNAc. Surface plasmon resonance analyses show that native MBL binds immobilized PGN with high avidity. Competition experiments also show that both native MBL and MBL(n/CRD), a 48-kDa recombinant trimeric fragment of MBL containing neck and carbohydrate recognition domains, have higher affinity for GlcNAc than for MurNAc. Protein arrays and ELISA show that PGN increases the secretion of TNF-alpha, IL-8, IL-10, MCP-2, and RANTES from PMA-stimulated human monocytic U937 cells. Interestingly, the presence of MBL together with PGN increases the production of IL-8 and RANTES, but reduces that of TNF-alpha. Our results indicate that Gram-positive bacterial is a biologically relevant ligand for MBL, and that the collectin preferentially binds to the GlcNAc moiety of the PGN via its C-type lectin domains. MBL inhibits PGN-induced production of proinflammatory cytokines while enhancing the production of chemokines by macrophages, which suggests that MBL may down-regulate macrophage-mediated inflammation while enhancing phagocyte recruitment.
The yeast acylglycerol acyltransferase LCA1 is a key component of Lands cycle for phosphatidylcholine turnover (2007)

Cellular phospholipids undergo deacylation and reacylation through a process known as Lands cycle. In this report, we provide evidence demonstrating that yeast YOR175c, herein designated as LCA1, encodes a key component of the Lands cycle, the acyl-CoA: lysophosphatidylcholine acyltransferase (LPCAT). Deletion of LCA1 resulted in a drastic reduction in LPCAT activity, while over expression led to a several fold increase in enzyme activity. We further show that disruption of LCA1 caused an enhanced production of glycerophosphorylcholine, a product of phosphatidylcholine (PC) deacylation and that the lysophosphatidic acid acyltransferase SLC1 was not involved in this process. Identification of LCA1 provides an essential molecular tool for further study of Lands cycle in PC turnover.
Inhibition of tumor promoter-induced ornithine decarboxylase activity by tannic acid and other polyphenols in mouse epidermis in vivo. (1991)

Naturally occurring plant phenols with antimutagenic and anticarcinogenic activities were tested for their abilities to inhibit the ornithine decarboxylase (ODC) response linked to skin tumor promotion by 12-O-tetradecanoylphorbol-13-acetate (TPA). Topical applications of tannic acid (TA) inhibit remarkably and in a dose-dependent manner TPA-induced ODC activity in mouse epidermis in vivo. This inhibitory effect of TA is dependent on the time of its administration relative to TPA. The induction of epidermal ODC activity by 8.5 nmol of TPA is inhibited maximally when 20 mumol of TA are applied topically to the skin 20 min before the tumor promoter. Gallic acid and several of its derivatives inhibit the ODC response to TPA to a lesser degree than TA. Ellagic acid is the least effective inhibitor tested. TA also inhibits the ODC-inducing activities of several structurally different tumor promoters and the greater ODC responses produced by repeated TPA treatments. The ability of TA to inhibit by 85% the ODC marker of skin tumor promotion suggests that TA and other polyphenols may be effective not only against tumor initiation and complete carcinogenesis but also against the promotion phase of tumorigenesis.
Implanted octacalcium phosphate is more resorbable than β‐tricalcium phosphate and hydroxyapatite (2001)

Our previous studies have suggested that synthetic octacalcium phosphate (OCP) could be resorbed and replaced by newly formed bone if implanted in rat skull defects. We hypothesized that the implanted OCP is more resorbable than other commonly used bone graft substitutes of calcium phosphate compounds, such as hydroxyapatite (HA) and beta-tricalcium phosphate (beta-TCP). To test the hypothesis, the present study was designed to compare histomorphometrically resorption of the implanted OCP, HA, and beta-TCP, which were kept in the experimental cranial defect of rats for a long term. A full thickness of standardized trephine defect was made in the rat parietal bone, and the same volume of granules of OCP, HA, and beta-TCP were implanted into the defect. Five specimens of each group were fixed 6 months after implantation. The percentage of remaining implants (r-Imp%) and newly formed bone (n-Bone%) in the defect was analyzed histomorphometrically. The statistical analysis showed that the r-Imp% of OCP was significantly lower than that of HA and beta-TCP. In contrast, the n-Bone% of OCP was significantly higher than that of HA and beta-TCP. The present study has shown that the implanted OCP in the rat cranial defect is more resorbable than the implanted beta-TCP and HA, whereas the implanted OCP enhances bone formation more than the implanted beta-TCP and HA.
Terminal Phosphate-Labeled Nucleotides with Improved Substrate Properties for Homogeneous Nucleic Acid Assays (2005)

Nucleotides with a dye attached to the terminal phosphate with four or more phosphates (tetra- or pentaphosphates) are superior substrates than the corresponding triphosphates for DNA and RNA polymerases. When fluorogenic dyes are directly attached to the terminal phosphate, they can be released by the action of polymerase and alkaline phosphatase. The released dye changes color and fluorescence properties. The fluorescent signal can also be amplified by using multiple labeled nucleotides to detect small amounts of template. We have explored the utility of these nucleotides in a variety of applications including homogeneous SNP detection methods, DNA sequencing, and quantitation of PCR and RCA.