gebhart/patrepeval huggingface dataset:
Culture confirmation of Escherichia coli serotype O157:H7 by direct immunofluorescence (1990)

An evaluation of a fluorescein-labeled, polyclonal, affinity-purified goat antibody to Escherichia coli serotype O157:H7 (Kirkegaard & Perry Laboratories Inc., Gaithersburg, Md.) was conducted to determine the efficacy of this research reagent for the rapid direct immunofluorescence identification of E. coli O157:H7 isolated from fecal specimens cultured on sorbitol-MacConkey (SMAC) agar. The E. coli O157:H7 fluorescent-antibody conjugate proved to be 100% sensitive and specific for the rapid identification of non-sorbitol-fermenting E. coli O157:H7 from SMAC agar inoculated with fecal specimens. The addition of SMAC agar to the battery of primary isolation media routinely used for fecal specimens resulted in the identification of 16 patients with E. coli O157:H7 disease from a total of 799 fecal specimens cultured during 1988.
Laser Electro-Optic System For Rapid Three-Dimensional (3-D) Topographic Mapping Of Surfaces (1981)

A method is described for high-resolution remote three-dimensional mapping of an unknown and arbitrarily complex surface by rapidly determining the three-dimensional locations of M x N sample points on that surface. Digital three-dimensional (3-D) locations defining a surface are acquired by (1) optically transforming a single laser beam into an (expanded) array of M x N individual laser beams, (2) illuminating the surface of interest with this array of M x N (simultaneous) laser beams, (3) using a programmable electro-optic modulator to very rapidly switch on and off specified subsets of laser beams, thereby illuminating the surface of interest with a rapid sequence of mathematical patterns (space code), (4) image recording each of the mathematical patterns as they reflect off the surface using (a) a wavelength-specific optically filtered video camera positioned at a suitable perspective angulation and (b) appropriate image memory devices, (5) analyzing the stored im-ages to obtain the 3-D locations of each of the M x N illuminated points on the surface which are visible to the camera or imaging device, and (6) determining which of the laser beams in the array do not provide reflec-tions visible to the imaging device. Space coding of the light beams allows automatic correlation of the camera image (of the reflected spot pattern from the surface) with the projected laser beam array, thus enabling triangulation of each illuminated surface point. Whereas ordinary laser rangefinders aim and project one laser beam at a time and expect to receive one laser beam reflection (bright dot image) at a time, the pres-ent system is optical (nonmechanical and vibration-free) and can collect all the data needed for high-resolution 3-D topographic mapping (of an M x N sample of surface points) with the projection of as few as 1 + log2N light patterns. In some applications involving a rapidly changing time-dependent environment, these 1 + log2N patterns can be projected simultaneously in different wavelengths to allow virtually
String-Matching with Automata. (1997)

. We present an algorithm to search in a text for the patterns of a regular set. Unlike many classical algorithms, we assume that the input of the algorithm is a deterministic automaton and not a regular expression. Our algorithm is based on the notion of failure function and mainly consists of efficiently constructing a new deterministic automaton. This construction is shown to be efficient. In particular, its space complexity is linear in the size of the obtained automaton. Key words: Finite automata, pattern-matching, strings. CR Classification: F.1.1, F.2.0, F.2.2, F.4.3 1. Introduction Pattern-matching consists of finding the occurrences of a set of strings in a text. Two general approaches have been used to perform this task given a regular expression r describing the patterns. Both require a preprocessing stage, which consists of constructing an automaton representing the set described by the regular expression A r, where A is the alphabet of the text. This automaton is th...
Correlations Between Apolipoprotein E ε4 Gene Dose and Whole Brain Atrophy Rates (2007)

Since APOE epsilon4 gene dose is associated with an increased risk of Alzheimer's disease and a younger median age at dementia onset, this study suggests an association between the risk of Alzheimer's disease and accelerated brain atrophy rates before the onset of cognitive impairment.
Detection and Quantification of Anthrax Lethal Factor in Serum by Mass Spectrometry (2007)

The lethal toxin produced during Bacillus anthracis infection is a complex of protective antigen, which localizes the toxin to the cell receptor, and lethal factor (LF), a zinc-dependent endoproteinase whose known targets include five members of the mitogen-activated protein kinase kinase (MAPKK) family of response regulators. We have developed a method for detecting functional LF in serum. Anti-LF murine monoclonal antibodies immobilized on magnetic protein G beads were used to capture and concentrate the LF from serum. The captured LF was exposed to an optimized MAPKK-based peptide substrate, which it hydrolyzed into two smaller peptides. The LF cleavage products were then analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS) and quantified by isotope dilution-MS. The entire analytical method can be performed in less than 4 h with detection of LF levels as low as 0.05 ng/mL. The method was used to quantify LF levels in serum from rhesus macaques infected with B. anthracis. Serum samples obtained at day 2 postinfection contained 30-250 ng/mL LF and illustrated the clear potential to detect LF earlier in the infection cycle. This method represents a highly specific and rapid diagnostic tool for early anthrax and has a potential additional role as a research tool for understanding toxemia and effects of medical countermeasures for anthrax.
Subscriber location in CDMA cellular networks (1998)

Subscriber radio location techniques are investigated for code-division multiple-access (CDMA) cellular networks. Two methods are considered for radio location: measured times of arrival (ToA) and angles of arrival (AoA). The ToA measurements are obtained from the code tracking loop in the CDMA receiver, and the AoA measurements at a base station (BS) are assumed to be made with an antenna array. The performance of the two methods is evaluated for both ranging and two-dimensional (2-D) location, while varying the propagation conditions and the number of BS's used for the location estimate.
Alloreactive murine CD8+ T cell clones secrete the Th1 pattern of cytokines. (1990)

A large panel of CD8+ mouse T cell clones expressed the cytokine synthesis pattern characteristic of Th1 clones. CD8+ clones synthesized IFN-gamma and lymphotoxin at levels similar to Th1 clones, whereas IL-2 was synthesized by only 50% of the clones and at significantly lower levels compared to Th1 clones. CD8+ clones also produced substantial amounts of granulocyte/macrophage-CSF, TY5, P500, and TNF-alpha which are expressed preferentially by Th1 clones and at lower levels by Th2 clones. The level of IL-3 produced by CD8+ clones was approximately 10% of that produced by Th1 and Th2 clones. Some CD8+ clones expressed low levels of the Th2-preferential product preproenkelphalin. None of the CD8+ clones expressed detectable levels of the Th2-specific products IL-4, IL-5, and P600, and the great majority did not express IL-6. The cytokine profile of CD8+ clones is representative of that secreted by activated normal CD8+ splenocytes, which includes IFN-gamma, low levels of IL-2 and IL-3 but no IL-4 or IL-5. Inasmuch as many Th1/Th2 functions are cytokine mediated, the striking similarity of the Th1 and CD8+ cytokine secretion patterns helps to explain why these two cell types share certain functions such as DTH, and also suggests that further common functions may be discovered in the future.
Possible applications of acyltransferases in oleotechnology (1993)

Les enzymes, en tant que catalyseurs, présentent de nombreux avantages : la spécificité, la régiosélectivité, l'énantiosélectivité et la catalyse inverse. Des applications potentielles existent dans les opérations de raffinage comme la démucilagination, la neutralisation, la décoloration. Et en lipochimie, dans les réactions d'hydrolyse, d'interestérification, d'estérification et d'acylation
The effect of activating mutations on dimerization, tyrosine phosphorylation and internalization of the macrophage colony stimulating factor receptor. (1994)

Oncogenic activation of the macrophage colony stimulating factor (M-CSF) receptor (c-Fms) requires mutation or truncation of the carboxyl terminus and specific amino acid substitutions in or near the fourth immunoglobulin (Ig)-like loop in the extracellular domain. Using a murine c-Fms system, we investigated the effect of C-terminal truncation, substitutions at amino acids 301 and 374 in the fourth Ig-like loop of the extracellular domain, or the combined mutations on individual steps in receptor activation. The mutations at amino acids 301 and 374 were necessary, but not sufficient, for receptor dimerization in the absence of M-CSF. Only receptors with a truncated C-terminus as well as the extracellular domain mutations dimerized efficiently in the absence of M-CSF, suggesting that the C-terminus of c-Fms also regulates receptor oligomerization. Truncation of the C-terminus alone did not cause receptor dimerization and did not activate the kinase enzymatic activity. Thus, truncation of the C-terminus did not activate receptor monomers in cis. Receptors with both a truncated C-terminus and the extracellular domain mutations underwent ligand-independent aggregation, transphosphorylation, and phosphorylation of cellular proteins, followed by rapid internalization and degradation. These results suggest that M-CSF binding to c-Fms initiates activation by inducing conformational changes in both the cytoplasmic C-terminal domain and the fourth Ig-like loop of the extracellular domain, leading to the formation of stable receptor dimers.
Target frequency and integration pattern for insertion and replacement vectors in embryonic stem cells. (1991)

Gene targeting has been used to direct mutations into specific chromosomal loci in murine embryonic stem (ES) cells. The altered locus can be studied in vivo with chimeras and, if the mutated cells contribute to the germ line, in their offspring. Although homologous recombination is the basis for the widely used gene targeting techniques, to date, the mechanism of homologous recombination between a vector and the chromosomal target in mammalian cells is essentially unknown. Here we look at the nature of gene targeting in ES cells by comparing an insertion vector with replacement vectors that target hprt. We found that the insertion vector targeted up to ninefold more frequently than a replacement vector with the same length of homologous sequence. We also observed that the majority of clones targeted with replacement vectors did not recombine as predicted. Analysis of the recombinant structures showed that the external heterologous sequences were often incorporated into the target locus. This observation can be explained by either single reciprocal recombination (vector insertion) of a recircularized vector or double reciprocal recombination/gene conversion (gene replacement) of a vector concatemer. Thus, single reciprocal recombination of an insertion vector occurs 92-fold more frequently than double reciprocal recombination of a replacement vector with crossover junctions on both the long and short arms.
Enhancement of DNA, cDNA synthesis and fidelity at high temperatures by a dimeric single-stranded DNA-binding protein (2003)

Bacterial single-stranded DNA-binding proteins (SSBs) are required for DNA replication and repair. We have over-expressed and purified the native form and two His-tagged fusions of the SSB from Thermus thermophilus (TthSSB). The three proteins were found as dimers in solution. They bound in vitro to single-stranded DNA specifically over a temperature range of 4-80 degrees C, and the wild-type protein could withstand incubation at 94 degrees C for 2 min. Addition of TthSSB to PCR halved the elongation time required for the DNA polymerases of T.thermophilus (Tth) and Pyrococcus furiosus (Pfu) to synthesise DNA fragments in PCRs. The presence of TthSSB increased the fidelity of the proof- reading-free DNA polymerase of T.thermophilus. TthSSB was also able to bind single-stranded RNA, allowing a dramatic enhancement of the reverse transcription activity of its cognate Tth DNA polymerase during cDNA synthesis.
Gamma (40-100 Hz) oscillation in the hippocampus of the behaving rat (1995)

The cellular generation and spatial distribution of gamma frequency (40-100 Hz) activity was examined in the hippocampus of the awake rat. Field potentials and unit activity were recorded by multiple site silicon probes (5- and 16-site shanks) and wire electrode arrays. Gamma waves were highly coherent along the long axis of the dentate hilus, but average coherence decreased rapidly in the CA3 and CA1 directions. Analysis of short epochs revealed large fluctuations in coherence values between the dentate and CA1 gamma waves. Current source density analysis revealed large sinks and sources in the dentate gyrus with spatial distribution similar to the dipoles evoked by stimulation of the perforant path. The frequency changes of gamma and theta waves positively correlated (40-100 Hz and 5-10 Hz, respectively). Putative interneurons in the dentate gyrus discharged at gamma frequency and were phase-locked to the ascending part of the gamma waves recorded from the hilus. Following bilateral lesion of the entorhinal cortex the power and frequency of hilar gamma activity significantly decreased or disappeared. Instead, a large amplitude but slower gamma pattern (25-50 Hz) emerged in the CA3-CA1 network. We suggest that gamma oscillation emerges from an interaction between intrinsic oscillatory properties of interneurons and the network properties of the dentate gyrus. We also hypothesize that under physiological conditions the hilar gamma oscillation may be entrained by the entorhinal rhythm and that gamma oscillation in the CA3-CA1 circuitry is suppressed by either the hilar region or the entorhinal cortex.
DRP1A Is Responsible for Vascular Continuity Synergistically Working with VAN3 in Arabidopsis (2005)

In most dicotyledonous plants, vascular tissues in the leaf have a reticulate venation pattern. We have isolated and characterized an Arabidopsis (Arabidopsis thaliana) mutant defective in the vascular network defective mutant, van3. van3 mutants show a discontinuous vascular pattern, and VAN3 is known to encode an ADP-ribosylation-factor-GTPase-activating protein that regulates membrane trafficking in the trans-Golgi network. To elucidate the molecular nature controlling the vein patterning process through membrane trafficking, we searched VAN3-interacting proteins using a yeast (Saccharomyces cerevisiae) two hybrid system. As a result, we isolated the plant Dynamin-Related Protein 1A (DRP1A) as a VAN3 interacting protein. The spatial and temporal expression patterns of DRP1AGUS and VAN3GUS were very similar. The subcellular localization of VAN3 completely overlapped to that of DRP1A. drp1a showed a disconnected vascular network, and the drp1a mutation enhanced the phenotype of vascular discontinuity of the van3 mutant in the drp1a van3 double mutant. Furthermore, the drp1 mutation enhanced the discontinuous vascular pattern of the gnom mutant, which had the same effect as that of the van3 mutation. These results indicate that DRP1 modulates the VAN3 function in vesicle budding from the trans-Golgi network, which regulates vascular formation in Arabidopsis.
Genetic Characterization of Antiplasmid Immunity through a Type III-A CRISPR-Cas System (2013)

Many prokaryotes possess an adaptive immune system encoded by clustered regularly interspaced short palindromic repeats (CRISPRs). CRISPR loci produce small guide RNAs (crRNAs) that, in conjunction with flanking CRISPR-associated (cas) genes, combat viruses and block plasmid transfer by an antisense targeting mechanism. CRISPR-Cas systems have been classified into three types (I to III) that employ distinct mechanisms of crRNA biogenesis and targeting. The type III-A system in Staphylococcus epidermidis RP62a blocks the transfer of staphylococcal conjugative plasmids and harbors nine cas-csm genes. Previous biochemical analysis indicated that Cas10, Csm2, Csm3, Csm4, and Csm5 form a crRNA-containing ribonucleoprotein complex; however, the roles of these genes toward antiplasmid targeting remain unknown. Here, we determined the cas-csm genes that are required for antiplasmid immunity and used genetic and biochemical analyses to investigate the functions of predicted motifs and domains within these genes. We found that many mutations affected immunity by impacting the formation of the Cas10-Csm complex or crRNA biogenesis. Surprisingly, mutations in the predicted nuclease domains of the members of the Cas10-Csm complex had no detectable effect on antiplasmid immunity or crRNA biogenesis. In contrast, the deletion of csm6 and mutations in the cas10 Palm polymerase domain prevented CRISPR immunity without affecting either complex formation or crRNA production, suggesting their involvement in target destruction. By delineating the genetic requirements of this system, our findings further contribute to the mechanistic understanding of type III CRISPR-Cas systems.
Phobic Anxiety Is Associated With Higher Serum Concentrations of Adipokines and Cytokines in Women With Diabetes (2009)

High levels of phobic anxiety are associated with increased levels of leptin and inflammatory markers, which may in part explain the previously observed relationship between anxiety and other psychosocial disorders with CVD.
Amino acids and peptides. X. Leu-enkephalin analogues containing a fluorinated aromatic amino acid. (1989)

Leu-enkephalin analogues containing a fluorinated derivative of Tyr1 or Phe4 were synthesized by the solid-phase method and their biological activities were studied. Fluorination of the p-position of Phe4 resulted in a marked potentiation of the inhibitory effect on electrically induced contractions of guinea-pig ileum (GPI) and mouse vas deferens (MVD). On the other hand, substitution of fluorine for the hydroxyl group of Tyr1 or introduction of a trifluoromethyl group at the p-position of Phe4 markedly reduced the inhibitory effect in both preparations. Fluorination of other positions of Tyr1 and Phe4 did not cause substantial changes in the activities as compared with Leu-enkephalin.
Induction of anti-recombinant human granulocyte-macrophage colony- stimulating factor (Escherichia coli-derived) antibodies and clinical effects in nonimmunocompromised patients (1994)

The pharmacokinetics of recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF), induction of anti-GM-CSF antibodies, and clinical effects related to the induction of the antibodies were analyzed in patients with metastatic colorectal carcinoma (CRC) who were not on chemotherapy (n = 20, nonimmunocompromised patients). rhGM-CSF (250 micrograms/m2/d; Escherichia coli-derived) was administered subcutaneously for 10 days every month for 4 months. Eight patients with multiple myeloma (MM) on intensive chemotherapy followed by rhGM-CSF treatment were also included (immunocompromised patients). After a single injection of GM-CSF at the first cycle in CRC patients, the maximum calculated concentration (Cmax) was 5.24 +/- 0.56 ng/mL; the half life (T1/2) was 2.91 +/- 0.8 hours; and the area under the concentration curve (AUC) was 30.86 +/- 6.03 hours x ng/mL (mean +/- SE). No anti-GM-CSF antibodies were detected. During the subsequent cycles, 95% of the CRC patients developed anti-GM-CSF IgG antibodies, which significantly altered the pharmacokinetics of rhGM-CSF at the third and fourth cycles with decreased Cmax (2.87 +/- 0.57 ng/mL; P < .05), T1/2 (1.57 +/- 0.2 hours; P < .05), and AUC (14.90 +/- 4.10 hours x ng/mL; P < .005). The presence of anti-GM-CSF antibodies significantly reduced the GM-CSF-induced enhancement of granulocytes, and there was a clear tendency for a decreased increment of monocytes. Antibodies diminished systemic side effects of rhGM-CSF. Only 1 of 8 MM patients showed a very low anti-GM-CSF antibody titer after GM-CSF therapy, as shown by enzyme-linked immunosorbent assay and Western blot. Therefore, in nonimmunocompromised patients, exogenous nonglycosylated GM-CSF induced an anti-GM-CSF IgG antibody response in practically all patients, which seemed to be of clinical significance. In immunocompromised patients, virtually no significant antibody response was shown.
Cell type‐specific regulation of major histocompatibility complex (MHC) Class I gene expression in astrocytes, oligodendrocytes, and neurons (1993)

Mechanisms of major histocompatibility complex (MHC) class I gene regulation in cells of the CNS have been studied in vitro. Astrocytes in primary cultures, but neither oligodendrocytes nor neurons, constitutively expressed cell surface MHC class I molecules. Interferon-gamma (IFN-gamma) treatment led to induction of MHC class I expression in astrocytes and oligodendrocytes but not in neurons. The conserved upstream sequence containing the juxtaposed nuclear factor (NF)-kappa B-like region I and IFN-response consensus sequence (ICS) constitutively enhanced MHC class I gene promoter activity in astrocytes, but not in oligodendrocytes or in neurons. Nuclear extracts from astrocytes, but not from oligodendrocytes and neurons, had a binding activity specific for the NF-kappa B-like region I sequence, indicating that constitutive expression of MHC class I genes is governed by the upstream region I enhancer and its binding factor. IFN-gamma treatment led to induction of MHC class I promoter activity in astrocytes and oligodendrocytes, but not in neurons. In accordance with this observation, a nuclear factor that binds to the ICS was induced in astrocytes and oligodendrocytes but not in neurons following IFN-gamma treatment. This study illustrates cell type-specific regulation of MHC class I genes in the CNS that correlates with the expression of DNA binding factors relevant to MHC class I gene transcription.
Thickness-Dependent Physical Properties of Coevaporated Cu4SnS4 Films (2013)

Cu 4 SnS 4 films of different thicknesses were prepared by thermal coevaporation technique on glass substrates at a constant substrate temperature of 400°C. The layer thickness was varied in the range 0.25–1 μ m. The composition analysis revealed that all the evaporated films were nearly stoichiometric. The XRD patterns indicated the presence of a strong (311) peak as the preferred orientation, following the orthorhombic crystal structure corresponding to Cu 4 SnS 4 films. Raman analysis showed a sharp peak at 317 cm −1 , also related to Cu 4 SnS 4 phase. The optical transmittance spectra suggested that the energy band gap decreased from 1.47 eV to 1.21 eV with increase of film thickness. The hot-probe test revealed that the layers had p-type electrical conductivity. A decrease of electrical resistivity was observed with the rise of film thickness.