gebhart/patrepeval huggingface dataset:
A Bifunctional Enzyme with L-Fucokinase and GDP-L-fucose Pyrophosphorylase Activities Salvages Free L-Fucose in Arabidopsis (2008)

Monomeric sugars generated during the metabolism of polysaccharides, glycoproteins, and glycolipids are imported to the cytoplasm and converted to respective nucleotide sugars via monosaccharide 1-phosphates, to be reutilized as activated sugars. Because L-fucose (L-Fuc) is activated mainly in the form of GDP derivatives in seed plants, the salvage reactions for L-Fuc are expected to be independent from those for Glc, Gal, L-arabinose, and glucuronic acid, which are activated as UDP-sugars. For this study we have identified, in the genomic data base of Arabidopsis, the gene (designated AtFKGP) of a bifunctional enzyme with similarity to both L-fucokinase and GDP-L-Fuc pyrophosphorylase. Recombinant AtFKGP (rAt-FKGP) expressed in Escherichia coli showed both L-fucokinase and GDP-L-Fuc pyrophosphorylase activities, generating GDP-L-Fuc from L-Fuc, ATP, and GTP as the starting substrates. Point mutations in rAtFKGPs at either Gly(133) or Gly(830) caused loss of GDP-L-Fuc pyrophosphorylase and l-fucokinase activity, respectively. The apparent K(m) values of L-fucokinase activity of rAtFKGP for L-Fuc and ATP were 1.0 and 0.45 mm, respectively, and those of GDP-L-Fuc pyrophosphorylase activity for L-Fuc 1-phosphate and GTP were 0.052 and 0.17 mm, respectively. The expression of AtFKGP was detected in most cell types of Arabidopsis, indicating that salvage reactions for free L-Fuc catalyzed by AtFKGP occur ubiquitously in Arabidopsis. Loss-of-function mutants with tDNA insertion in AtFKGP exhibited higher accumulation of free L-Fuc in the soluble fraction than the wild-type plant. These results indicate that AtFKGP is a bifunctional enzyme with L-fucokinase and GDP-L-Fuc pyrophosphorylase activities, which salvages free L-Fuc in Arabidopsis.
Increased nerve growth factor levels in the urinary bladder of women with idiopathic sensory urgency and interstitial cystitis (1997)

The increased level of NGF may explain several clinical and pathological features in these conditions, including sensitization of nociceptor fibres and increased numbers of mast cells. We propose that anti-NGF treatment may be a rational and effective treatment in intractable bladder pain.
Highly constrained backprojection for time‐resolved MRI (2005)

Recent work in k-t BLAST and undersampled projection angiography has emphasized the value of using training data sets obtained during the acquisition of a series of images. These techniques have used iterative algorithms guided by the training set information to reconstruct time frames sampled at well below the Nyquist limit. We present here a simple non-iterative unfiltered backprojection algorithm that incorporates the idea of a composite image consisting of portions or all of the acquired data to constrain the backprojection process. This significantly reduces streak artifacts and increases the overall SNR, permitting decreased numbers of projections to be used when acquiring each image in the image time series. For undersampled 2D projection imaging applications, such as cine phase contrast (PC) angiography, our results suggest that the angular undersampling factor, relative to Nyquist requirements, can be increased from the present factor of 4 to about 100 while increasing SNR per individual time frame. Results are presented for a contrast-enhanced PR HYPR TRICKS acquisition in a volunteer using an angular undersampling factor of 75 and a TRICKS temporal undersampling factor of 3 for an overall undersampling factor of 225.
Rough neural intelligent approach for image classification: A case of patients with suspected breast cancer (2007)

The objective of this paper is to introduce a rough neural intelligent approach for rule generation and image classification. Hybridization of intelligent computing techniques has been applied to see their ability and accuracy to classify breast canc
Post-route optimization for improved yield using a rubber-band wiring model (1997)

This paper presents a unique approach to improve yield given a routed layout. Currently after routing has been completed and compacted, it generally proceeds to verification without further modifications. However, to improve manufacturability, we introduce a concept called even wire distribution, a key element of the SURF physical design tool. To alleviate congestion, we first move vias and wires torwards less dense areas in a manner which preserves the existing wiring paths. Depending on locally available area, we then increase wire spacing to reduce defect sensitivity, without changing the area of the design. Carafe, an inductive fault analysis tool is used to evaluate the new layout.
Expression of the rat GLUT1 glucose transporter in the yeast Saccharomyces cerevisiae (1996)

We expressed the rat GLUT1 facilitative glucose transporter in the yeast Saccharomyces cerevisiae with the use of a galactose-inducible expression system. Confocal immunofluorescence microscopy indicated that a majority of this protein is retained in an intracellular structure that probably corresponds to endoplasmic reticulum. Yeast cells expressing GLUT1 exhibited little increase in glucose-transport activity. We prepared a crude membrane fraction from these cells and made liposomes with this fraction using the freeze-thaw/sonication method. In this reconstituted system, D-glucose-transport activity was observed with a Km for D-glucose of 3.4 +/- 0.2 mM (mean +/- S.E.M.) and was inhibited by cytochalasin B (IC50= 0.44 +/- 0.03 microM), HgCl2 (IC50)= 3.5 +/- 0.5 microM), phloretin (IC50= 49 +/- 12 microM) and phloridzin (IC50= 355 +/- 67 microM). To compare these properties with native GLUT1 we made reconstituted liposomes with a membrane fraction prepared from human erythrocytes, in which the Km of D-glucose transport and ICs of these inhibitors were approximately equal to those obtained with GLUT1 made by yeast. When the relative amounts of GLUT1 in the crude membrane fractions were measured by quantitative immunoblotting, the specific activity of the yeast-made GLUT1 was 110% of erythrocyte GLUT1, indicating that GLUT1 expressed in yeast is fully active in glucose transport.
Purification and characteristics of the streptococcal chemotactic factor inactivator (1985)

The biochemical and immunological characteristics of the chemotactic factor inactivator of group A streptococci (SCFI) were examined. SCFI was extracted from intact M+ bacteria by limited trypsin digestion and purified sequentially by ammonium sulfate fractionation, hydrophobic interaction chromatography, and anion-exchange chromatography. SCFI activity was associated with multiple species as indicated by gel permeation chromatography and DEAE high-pressure liquid chromatography analyses. Polyacrylamide gel electrophoresis of the column-purified protein also demonstrated a high degree of molecular heterogeneity, with most of the material in a 103,000 to 114,000 Mr cluster. SCFI activity was sensitive to destruction by several proteolytic enzymes, and polyclonal antiserum to SCFI was able to neutralize its antichemotactic activity. Two-dimensional immunoelectrophoresis of SCFI indicated that the various copurified species were immunologically cross-reactive and indicated a high degree of antigenic homogeneity within the preparation. Western blot analysis of crude detergent extracts of M+ bacteria identified a major antigenic species corresponding to 135,000 Mr and a less abundant species of 137,000 Mr. SCFI antiserum was not reactive with M protein, and therefore SCFI appeared to be a distinct molecule, despite its close association with the M+ phenotype.
Concentration-dependent patterning of the Xenopus ectoderm by BMP4 and its signal transducer Smad1 (1997)

Morphogens are thought to establish pattern in early embryos by specifying several cell fates along a gradient of concentration; a well-studied example is the Drosophila protein decapentaplegic (DPP) acting in the wing disc. Recent work has established that bone morphogenetic protein 4 (BMP4), the vertebrate homologue of DPP, controls the fundamental choice between neural and epidermal fates in the vertebrate ectoderm, under the control of antagonists secreted by the organizer region of the mesoderm. We now show that BMP4 can act as a morphogen, evoking distinct responses in Xenopus ectodermal cells at high and low concentrations, in a pattern consistent with the positions of the corresponding cell types in the embryo. Moreover, this complex cellular response to extracellular BMP4 concentration does not require subsequent cell-cell communication and is thus direct, as required of a classical morphogen. We also show that the same series of cell types--epidermis, cement gland and neural tissue--can be produced by progressively inhibiting endogenous BMP signaling with specific antagonists, including the organizer factor noggin. Finally, expression of increasing doses of the signal transduction molecule Smad1 accurately reproduces the response to BMP4 protein. Since Smads have been shown to act in the nucleus, this finding implies a direct translation of extracellular morphogen concentration into transcription factor activity. We propose that a graded distribution of BMP activity controls the specification of several cell types in the gastrula ectoderm and that this extracellular gradient acts by establishing an intracellular and then nuclear gradient of Smad activity.
Comparison of the 5′ nuclease activities of Taq DNA polymerase and its isolated nuclease domain (1999)

Many eubacterial DNA polymerases are bifunctional molecules having both polymerization (P) and 5' nuclease (N) activities, which are contained in separable domains. We previously showed that the DNA polymerase I of Thermus aquaticus (TaqNP) endonucleolytically cleaves DNA substrates, releasing unpaired 5' arms of bifurcated duplexes. Here, we compare the substrate specificities of TaqNP and the isolated 5' nuclease domain of this enzyme, TaqN. Both enzymes are significantly activated by primer oligonucleotides that are hybridized to the 3' arm of the bifurcation; optimal stimulation requires overlap of the 3' terminal nucleotide of the primer with the terminal base pair of the duplex, but the terminal nucleotide need not hybridize to the complementary strand in the substrate. In the presence of Mn2+ ions, TaqN can cleave both RNA and circular DNA at structural bifurcations. Certain anti-TaqNP mAbs block cleavage by one or both enzymes, whereas others can stimulate cleavage of nonoptimal substrates.
Effect of Nucleotide Restriction and Supplementation on Resistance to Experimental Murine Candidiasis (1988)

The influence of dietary nucleotides on susceptibility to candidiasis in mice was studied using two criteria: animal survival and recovery of viable Candida albicans organisms from the kidney and spleen. One-month-old mice were placed on one of five diets with varying nucleotide content. The results show that mice maintained on a nucleotide-free diet (NF) exhibit a significantly decreased mean survival time and a significantly increased viable organism recovery in the spleen following intravenous injection of graded inocula of C. albicans compared to mice fed diets containing RNA or uracil as a nucleotide source.
Two acyl-coenzyme A oxidases in peroxisomes of the yeast Candida tropicalis: primary structures deduced from genomic DNA sequence. (1986)

We report the complete nucleotide sequence of two genes encoding major peroxisomal polypeptides (PXPs) of Candida tropicalis. One, POX4, encodes PXP-4, which is the most abundant polypeptide in cells grown on oleic acid, and the other, POX5, is the gene for PXP-5. Each of the two polypeptides was found to be the subunit of a distinct long-chain acyl-coenzyme A oxidase: acyl-CoA oxidase II (PXP-4) or acyl-CoA oxidase I (PXP-5). Both the genes had no intron and gave a single open reading frame. The NH2-terminal sequences, except the initiator methionine, and the calculated molecular weights of the deduced polypeptides were consistent with those of the respective PXPs. Well-conserved sequences of 12 and 16 hydrophobic amino acids were present in the middle of the polypeptide, instead of at the NH2 terminus, and may be internal signal sequences for the peroxisomal location of PXPs. Although the two polypeptides were significantly homologous throughout their sequences, the local homologies in two regions out of five were markedly diverged from the average (63%); the homology in the second region was 93%, whereas that in the fourth one was only 24%. The implications of this finding are discussed in respect to the multiplicity of peroxisomal enzymes and the presence of multifunctional proteins in peroxisomes.
Optical reflectometry with micrometer resolution for the investigation of integrated optical devices (1989)

An optical time-domain reflectometry (OTDR) system using an infrared subpicosecond pulse source in conjunction with balanced heterodyne detection is discussed. Experimental results show a density of more than 100 dB and a resolution of 60 mu m in air. Taking advantage of the large tuning range of the laser system, it is possible to improve the resolution to less than 10 mu m. The applicability of the OTDR system for the diagnostics of integrated optical devices is demonstrated for a simple GaAs waveguide structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bone Marrow as a Potential Source of Hepatic Oval Cells (1999)

Bone marrow stem cells develop into hematopoietic and mesenchymal lineages but have not been known to participate in production of hepatocytes, biliary cells, or oval cells during liver regeneration. Cross-sex or cross-strain bone marrow and whole liver transplantation were used to trace the origin of the repopulating liver cells. Transplanted rats were treated with 2-acetylaminofluorene, to block hepatocyte proliferation, and then hepatic injury, to induce oval cell proliferation. Markers for Y chromosome, dipeptidyl peptidase IV enzyme, and L21-6 antigen were used to identify liver cells of bone marrow origin. From these cells, a proportion of the regenerated hepatic cells were shown to be donor-derived. Thus, a stem cell associated with the bone marrow has epithelial cell lineage capability.
A more efficient distance vector routing algorithm (2002)

A more efficient distance vector routing algorithm (EDVA) for computer networks is presented. EDVA is based on enhancements to two classes of distance vector algorithms: the path finding algorithms that report complete path information incrementally, and the diffusing update algorithm (DUAL) which is used in Cisco's Enhanced Interior Gateway Routing Protocol (EIGRP) and is based on diffusing computations for internodal synchronization. EDVA operates by specifying a distance, a feasible distance, a predecessor and diffusing hops to each destination. This information is used together with diffusing computations of limited span to avoid routing-table loops. The correctness of EDVA is discussed, and its benefits compared with DUAL and path finding algorithms are illustrated with simple examples.
New home telephone system using Japanese Home Bus System standard (1989)

A home telephone system was developed as the first mass product for a basic home information system using the Japanese Home Bus System standard. The home telephone system offers not only communication services but also housekeeping services such as home security and remote control and management of call charges. The telephone sets and optional devices which realized these services were designed to improve the man-machine interfaces and the cost. The system construction, telephone sets, and optional devices are also designed to ensure future system expansion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
MHD stability of a hot rotating plasma: A brief review of PSP-2 experiments (2009)

The paper presents a review of theoretical and experimental studies of plasma stability in systems with a rotating plasma (devices with crossed E×B fields) carried out in 1975–1985 at the Institute of Nuclear Physics, Siberian Branch of the Russian Academy of Sciences. The first group of studies involves numerical simulations based on the classical work by M. Rosenbluth and A. Simon. The conditions in which the centrifugal flute instability in the plasma of such devices is absent were investigated. It is shown that, in order for this instability to be suppressed, it is necessary that the following two requirements be satisfied simultaneously: azimuthal plasma rotation should be sheared and the longitudinal electric current should be strong enough (the so-called line-tying effect). The second group of studies involves experiments in the PSP-02 and PSP-2 devices. The main experiments were carried out in PSP-2 at proton energies of 15–20 keV (30–40 keV in the laboratory frame) and electron energies of a few kiloelectronvolts, the plasma potential being up to 0.4 MV. The possibility of completely suppressing centrifugal flute instability was demonstrated experimentally for the first time. In the stable (classical) regime, the only processes are ionization and proton charge exchange. When centrifugal instability is suppressed, no other types of MHD plasma activity are observed.
Molecular Cloning and Ethylene-Inducible Expression ofChib1 Chitinase from Soybean (Glycine max(L.) Merr.) (1999)

A soybean seed-specific PR-8 chitinase, named Chib2, has a markedly extended C-terminal segment compared to other plant Chib1 homologues of the PR-8 chitinase family known to date. To further characterize the molecular structure and the expression pattern of this chitinase family, we cloned two typical Chib1-similar cDNAs (Chib1-1 and Chib1-2) from soybeans by PCR-cloning techniques. The deduced primary sequence of Chib1-1 chitinase is composed of a signal peptide segment (26 amino acid residues) and a mature 273 amino acid sequence (calculated molecular mass 28,794, calculated pI 3.7). This Chib1-1 enzyme is more than 90% identical to Chib1-2 chitinase but is below 50% identical to Chib2 enzyme. Thus, we confirmed the occurrence of two distinct classes, Chib1 and Chib2 in the plant PR-8 chitinase family. The Chib1 genes, interrupted by one intron, were found to be up-regulated in response to ethylene in stems and leaves, but scarcely expressed in developing soybean seeds. Chib1 chitinases may be responsible for protecting the plant body from various pathogenic attacks.
IL‐10‐Producing T Regulatory Type 1 Cells and Oral Tolerance (2004)

Oral tolerance is mediated by multiple mechanisms such as anergy and/or active suppression of antigen-specific effector T cells by T regulatory (Tr) cells. Among the CD4(+) Tr cells, T regulatory type 1 cells (Tr1) have been shown to downmodulate immune responses through production of the immunosuppressive cytokines IL-10 and TGF-beta. Human Tr1 cells can be induced to differentiate in vitro by IL-10 1 IFN-alpha or after stimulation by immature dendritic cells (DCs) or DCs rendered tolerogenic by exposure to immunomodulatory compounds. Murine Tr1 cells can be induced to differentiate in vitro by activating naive CD4(+) T cells in the presence of high doses of IL-10. Several protocols for induction of oral tolerance, including oral administration of the antigen with IL-10, have been shown to induce antigen-specific Tr1 cells that suppress undesired immune responses toward self-antigens, allergens, and food antigens. Overall, these data demonstrate that IL-10-producing Tr1 cells play a central role in the induction of oral as well as systemic tolerance.
Therapeutical targeting of nucleic acid-sensing Toll-like receptors prevents experimental cerebral malaria (2011)

Excessive release of proinflammatory cytokines by innate immune cells is an important component of the pathogenic basis of malaria. Proinflammatory cytokines are a direct output of Toll-like receptor (TLR) activation during microbial infection. Thus, interference with TLR function is likely to render a better clinical outcome by preventing their aberrant activation and the excessive release of inflammatory mediators. Herein, we describe the protective effect and mechanism of action of E6446, a synthetic antagonist of nucleic acid-sensing TLRs, on experimental cerebral malaria (ECM) induced by Plasmodium berghei ANKA. We show that in vitro, low doses of E6446 specifically inhibited the activation of human and mouse TLR9. Tenfold higher concentrations of this compound also inhibited the human TLR8 response to single-stranded RNA. In vivo, therapy with E6446 diminished the activation of TLR9 and prevented the exacerbated cytokine response observed during acute Plasmodium infection. Furthermore, severe signs of ECM, such as limb paralysis, brain vascular leak, and death, were all prevented by oral treatment with E6446. Hence, we provide evidence that supports the involvement of nucleic acid-sensing TLRs in malaria pathogenesis and that interference with the activation of these receptors is a promising strategy to prevent deleterious inflammatory responses that mediate pathogenesis and severity of malaria.
Viruses of Lower Vertebrates (2001)

Viruses of lower vertebrates recently became a field of interest to the public due to increasing epizootics and economic losses of poikilothermic animals. These were reported worldwide from both wildlife and collections of aquatic poikilothermic animals. Several RNA and DNA viruses infecting fish, amphibians and reptiles have been studied intensively during the last 20 years. Many of these viruses induce diseases resulting in important economic losses of lower vertebrates, especially in fish aquaculture. In addition, some of the DNA viruses seem to be emerging pathogens involved in the worldwide decline in wildlife. Irido‐, herpes‐ and polyomavirus infections may be involved in the reduction in the numbers of endangered amphibian and reptile species. In this context the knowledge of several important RNA viruses such as orthomyxo‐, paramyxo‐, rhabdo‐, retro‐, corona‐, calici‐, toga‐, picorna‐, noda‐, reo‐ and birnaviruses, and DNA viruses such as parvo‐, irido‐, herpes‐, adeno‐, polyoma‐ and poxviruses, is described in this review.
Effect of Mutant α-Synuclein on Dopamine Homeostasis in a New Human Mesencephalic Cell Line (2002)

Mutations in alpha-synuclein have been linked to rare, autosomal dominant forms of Parkinson's disease. Despite its ubiquitous expression, mutant alpha-synuclein primarily leads to the loss of dopamine-producing neurons in the substantia nigra. alpha-Synuclein is a presynaptic nerve terminal protein of unknown function, although several studies suggest it is important for synaptic plasticity and maintenance. The present study utilized a new human mesencephalic cell line, MESC2.10, to study the effect of A53T mutant alpha-synuclein on dopamine homeostasis. In addition to expressing markers of mature dopamine neurons, differentiated MESC2.10 cells are electrically active, produce dopamine, and express wild-type human alpha-synuclein. Lentivirus-induced overexpression of A53T mutant alpha-synuclein in differentiated MESC2.10 cells resulted in down-regulation of the vesicular dopamine transporter (VMAT2), decreased potassium-induced and increased amphetamine-induced dopamine release, enhanced cytoplasmic dopamine immunofluorescence, and increased intracellular levels of superoxide. These results suggest that mutant alpha-synuclein leads to an impairment in vesicular dopamine storage and consequent accumulation of dopamine in the cytosol, a pathogenic mechanism that underlies the toxicity of the psychostimulant amphetamine and the parkinsonian neurotoxin 1-methyl-4-phenylpyridinium. Interestingly, cells expressing A53T mutant alpha-synuclein were resistant to amphetamine-induced toxicity. Because extravesicular, cytoplasmic dopamine can be easily oxidized into reactive oxygen species and other toxic metabolites, mutations in alpha-synuclein might lead to Parkinson's disease by triggering protracted, low grade dopamine toxicity resulting in terminal degeneration and ultimately cell death.