gebhart/patrepeval huggingface dataset:
Gene Cloning and Characterization of an Acidic Xylanase fromAcidobacterium capsulatum (1998)

The gene xynA encoding an acid endo-beta-1,4-xylanase from an acidophilic bacterium, Acidobacterium capsulatum 161, was cloned and expressed in Eschrichia coli. The nucleotide sequence of the 1.6-kb DNA fragment containing xynA was analyzed, revealing an open reading frame of 1,215 bp encoding a peptide of 405 amino acid residues. The deduced amino acid sequence of XynA was very similar to other xylanases that are from the glycosyl hydrolase family 10. XynA was purified to homogeneity by SDS-polyacrylamide gel electrophoresis from E. coli transformants. The molecular mass and isoelectric point of XynA were 41 kDa and 7.3, respectively. The xylanase activity of the cloned XynA is an endo-acting enzyme that shows optimal activity at pH 5.0 and 65 degrees C, and is stable pH between 3.0 and 8.0. The K(m) and Vmax with oat spelt xylan as a substrate at pH 5.0 and 30 degrees C are 3.5 mg/ml and 403 mumol/min/mg.
Increased disruption of sperm plasma membrane at sperm immobilization promotes dissociation of perinuclear theca from sperm chromatin after intracytoplasmic sperm injection in pigs (2005)

The effects of sperm-immobilization methods on decondensation of sperm chromatin and retention of subacrosomal sperm perinuclear theca (SAR-PT) after intracytoplasmic sperm injection (ICSI) were examined in pigs. Sperm membrane damage caused by different immobilization methods by rubbing with a micropipette without piezo pulses (R), or with a low (L) or high (H) intensity of piezo pulses while rubbing, was assessed by the time required for staining of sperm heads with eosin Y solution. The average time for staining of sperm heads immobilized by the R, L or H treatments was 76, 41 or 26 s, respectively. The fertilization rate following ICSI was increased by sperm immobilization by piezo pulses compared with R, but increased intensity of pulses from L to H did not cause further improvements (29, 48 and 47%, respectively). An immunofluorescence study revealed that H immobilization promoted the dissociation of SAR-PT from sperm chromatin compared with L and R, and it increased the frequency of male pronuclear formation in which chromatin appeared uniformly decondensed. With in vitro fertilization (IVF), SAR-PT disassembled coordinately with sperm chromatin decondensation and it was not detectable around male pronuclei. This was different from most of the oocytes after ICSI in which remnants SAR-PT were detected adjacent to male pronuclei. We concluded that increased damage on the sperm plasma membrane at immobilization improved fertilization rates and decondensation of sperm chromatin after ICSI due to the accelerated dissociation of SAR-PT from the sperm nucleus. Also, the behavior of SAR-PT after ICSI was different from that observed in oocytes after IVF.
Effect of Beraprost Sodium (TRK-100) on Erythrocyte Deformability, Blood Viscosity and Thrombus Formation in Rats (1990)

Stable prostacyclin (PGI2) analogue, beraprost sodium (sodium (±)-(1R*, 2R*, 3aS*, 8bS*)-2, 3, 3a, 8b-tetrahydro-2-hydroxy-1-[(E)-(3S*)-3-hydroxy-4-methyl-1-octen-6-ynyl]-1H-cyclopenta [b] benzofuran-5-butyrate, TRK-100) had been reported to inhibit aggregation of platelets and dilate blood vessels. In this report, the effect of beraprost sodium (beraprost) on haemorheological parameters such as erythrocyte deformability and blood viscosity, and activity of blood coagulation system such as activated partial thromboplastin time and prothrombin time were measured in normal rats. Effect of orally administered beraprost on experimentally induced disorders of peripheral circulation such as femoral artery occlusion and venous thrombosis model in rats were assessed.Erythrocyte deformability was increased by beraprost from the concentration of 23.8 up to 2380nM in vitro (Fig. 1), and from 176 up to 560μg/kg/day after 7 days consecutive administration to normal rats ex vivo (Fig. 2).Occlusion of rat femoral artery by insertion of polyethylene tube induces reproducible lesions in the toe (Fig. 7) and elevation of blood and plasma viscosity (Tab. 1). Blood viscosity of normal rats was not affected by beraprost up to 10μM in vitro (Fig. 3) or up to 100μg/kg ex vivo (Fig. 4). However, at the dose of 30μg/kg, beraprost normalized blood viscosity of femoral artery occluded rats (Fig. 8).In the model of stasis induced venous thrombosis, beraprost decreased the weight of thrombus in the inferior vena cava of rats. The effect was dose-dependent at range from 30 to 100μg/kg (Fig. 9). It, however, showed no effects on blood coagulation system of rats ex vivo at the dose which decreased thrombus weight (Fig. 6), and at the concentration range of 23.8nM to 238μM in human plasma in vitro (Fig. 5).Above results suggest that beraprost may contribute to the improvement of haemorheological impairment and prevention of thrombus formation in the disorder of peripheral circulation.
The LDL Receptor (2009)

In this article, the history of the LDL receptor is recounted by its codiscoverers. Their early work on the LDL receptor explained a genetic cause of heart attacks and led to new ways of thinking about cholesterol metabolism. The LDL receptor discovery also introduced three general concepts to cell biology: receptor-mediated endocytosis, receptor recycling, and feedback regulation of receptors. The latter concept provides the mechanism by which statins selectively lower plasma LDL, reducing heart attacks and prolonging life.
Dihydroxyacetone Variants in the Organocatalytic Construction of Carbohydrates:  Mimicking Tagatose and Fuculose Aldolases (2006)

Dihydroxyacetone variants have been explored as donors in organocatalytic aldol reactions with various aldehyde and ketone acceptors. The protected form of dihydroxyacetone that was chosen for in-depth study was 2,2-dimethyl-1,3-dioxan-5-one, 1. Among the catalysts surveyed here, proline proved to be superior in terms of yield and stereoselectivities in the construction of various carbohydrate scaffolds. In a fashion analogous to aldolase enzymes, the de novo preparation of l-ribulose, l-lyxose, d-ribose, d-tagatose, 1-amino-1-deoxy-d-lyxitol, and other carbohydrates was accomplished via the use of 1 and proline. In reactions using 2,2-dimethyl-1,3-dioxan-5-one 1 as a donor, (S)-proline can be used as a functional mimic of tagatose aldolase, whereas (R)-proline can be regarded as an organocatalytic mimic of fuculose aldolase.
Predictors of Clinical Outcome in Schizophrenic Patients Responding to Clozapine (2003)

Many of the patients who respond better to clozapine (CLZ) than to typical antipsychotics still have residual psychopathology, but CLZ drug resistance data are lacking. The aim of this study was to evaluate the possible predictive factors of a clinical response to CLZ in a group of 20 schizophrenic patients (DSM-IV: 13 males and 7 females with a mean age of 35.5 years +/- 7.1 SD) resistant to typical antipsychotics but CLZ responders as assessed by the Brief Psychiatric Rating Scale (BPRS) (>20% improvement). After a 1-week washout period, CLZ was started at a dose of 25 mg/d, which was increased by the third week up to a maximum of 600 mg/d (mean 365.00 +/- 129.88 mg/d SD) and remained unchanged until the end of the study (week 8). The patients showed a significant improvement in the mean scores of the rating scales for positive (SAPS) and negative symptoms of schizophrenia (Scale for the Assessment of Negative Symptoms, SANS) (P < 0.003, P < 0.02). All of the patients included in the study were BPRS responders; 65% were also SAPS and 75% SANS responders (>20% improvement). The improvement in the SANS score was significantly greater among the female patients (P < 0.05). The SAPS and SANS responders had a significantly higher mean metabolic ratio [MR = (NCLZ/CLZ)] than the nonresponders (P < 0.01), and the percentage of improvement significantly correlated with the increase in MR. This finding suggests that the individual pharmacogenetics indicated by metabolic capacity may be related to clinical response. All of the patients showed a reduction in white blood cell counts, but this was significantly less in the SANS responders than the SANS nonresponders (P = 0.047). The SAPS responders had significantly lower neutrophil counts than the nonresponders (P = 0.03). Our results seem to suggest the importance of pharmacodynamic, constitutional, and genetic data over strict pharmacokinetics in determining the clinical response to CLZ.
Chemistry of clays and clay minerals (1987)

Bringing together information widely distributed throughout scientific and industrial journals, here is an overview of the chemical consititution and properties of clay minerals and the environmental conditions that lead to their formation. Provides a detailed picture of the chemical consititution of the eight main groups of clay minerals containing silica and of the non-siliceous oxide clays. The central section of the book deals with the properties of clays: their colloidal behavior, cation exchange, interaction with water, reactions on heating, catalytic properties, and reactions with organic compounds. Also discusses the chemical conditions that favor the formation of clays and their evolution or decomposition into other materials.
Structural and Enzymatic Studies of the T4 DNA Replication System (1989)

In this paper we report a detailed enzymatic characterization of the interaction of the polymerase accessory protein complex of the T4 DNA replication system with the various nucleic acid cofactors that activate the ATPase of the complex. We show that the ATPase activity of the T4 coded gene 44/62 protein complex is stimulated synergistically by binding of DNA and T4 gene 45 protein and that the level of ATPase activation appears to be directly correlated with the binding of nucleic acid cofactor. Binding of any partially or completely single-stranded DNA to the complete accessory protein complex increases the catalytic activity (as measured by Vmax) while decreasing the binding affinity for the ATP substrate. While single-stranded DNA is a moderately effective cofactor, we find that the optimal nucleic acid-binding site for the complex is the primer-template junction, rather than single-stranded DNA ends as previously reported in the literature. Gene 45 protein plays an essential role in directing the specificity of binding to primer-template sites, lowering the Km for primer-template sites almost 1000-fold, and increasing Vmax 100-fold, compared with the analogous values for gene 44/62 protein alone. The most effective primer-template site for binding and enzymatic activation has the physiologically relevant recessed 3'-OH configuration and an optimal size in excess of 18 base pairs of duplex DNA. We find that the chemical nature of the primer terminus (i.e. 3'-OH or 3'-H) does not affect the extent of ATPase activation and that binding of the polymerase accessory protein complex to DNA cofactors is salt concentration dependent but appreciably less so when the activating DNA is a primer-template junction. Finally, we show that the gene 32 protein (T4 coded single-stranded DNA-binding protein) can compete with the polymerase accessory protein complex for single-stranded DNA but not for the primer-template junction activation sites. The implications of these results for the structure and function of the polymerase accessory protein complex within the T4 DNA replication system are discussed.
Electrocatalytic reduction of carbon dioxide on a cobalt tetrakis(4-aminophenyl)porphyrin modified electrode in BMImBF4 (2014)

Electro-catalytic reduction of CO<sub>2</sub>at −0.8 V<italic>vs.</italic>Ag/AgCl has been studied with poly-Co(<sc>ii</sc>)-porphyrin on ITO in BMImBF<sub>4</sub>as reaction media.
Counting Markov Types, Balanced Matrices, and Eulerian Graphs (2012)

The method of types is one of the most popular techniques in information theory and combinatorics. Two sequences of equal length have the same type if they have identical empirical distributions. In this paper, we focus on Markov types, that is, sequences generated by a Markov source (of order one). We note that sequences having the same Markov type share the same so-called balanced frequency matrix that counts the number of distinct pairs of symbols. We enumerate the number of Markov types for sequences of length over an alphabet of size . This turns out to be asymptotically equivalent to estimating the number of the balanced frequency matrices, the number of integer solutions of a system of linear Diophantine equations, and the number of connected Eulerian multigraphs. For fixed , we prove that the number of Markov types is asymptotically equal to d(m) n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sup> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-m</sup> /(m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> -m)! where we give an integral representation for d(m). For m →∞, we conclude that asymptotically the number of types is equivalent to √2m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3m/2</sup> e <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sup> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2m2</sup> 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sup> π <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m/2</sup> n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m2</sup> -m provided that m = o(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/4</sup> ). These findings are derived by analytical techniques ranging from analytic combinatorics, to multidimensional generating functions, to the saddle point method.
Nonspecific and Candida-Specific Immune Responses in Mice Suppressed by Chronic Administration of Anti-μ (1988)

CBA/J mice were immunosuppressed by repeated administration of goat antibody specific for mu chain of immunoglobulin M (IgM) and tested for nonspecific and Candida albicans-specific immune responses. Immunosuppression was demonstrated by a dramatic reduction in the number of antibody-forming cells in the spleens of anti-mu-treated mice when immunized with sheep erythrocytes, by greatly reduced in vitro responsiveness of both spleen and lymph node lymphocytes from anti-mu-treated mice to lipopolysaccharide, and by a large reduction in the number of splenic IgM-positive cells. T cell function, on the other hand, appeared to be relatively unaltered in anti-mu-treated animals, in the cytotoxic T lymphocyte activity against an allogeneic target was similar in splenocyte cultures from anti-mu- and mock-treated animals, and splenic and lymph node lymphocytes proliferated in response to concanavalin A in a lymphocyte stimulation assay. Moreover, Candida-specific delayed hypersensitivity to two different Candida antigens, one cell wall-derived (GP) and the other cell membrane-derived (BEX), was of comparable intensity in immunosuppressed and normal animals. When anti-mu- and mock-treated mice were immunized by the cutaneous inoculation of viable C. albicans blastospores and then challenged intravenously to assess the development of protective immunity, only mock-treated animals, male and female, had significant (p less than or equal to 0.05) protective responses demonstrable by reduction in the number of colony-forming units cultured from their kidneys 28 days after intravenous challenge. If consideration was given to the number of animals which had cleared Candida completely from the kidney, however, there appeared to be protective responses operative in the female anti-mu-treated animals as well. Neither anti-mu-treated males nor females, when immunized and challenged with C. albicans, produced Candida-specific antibody detectable by counterimmunoelectrophoresis, whereas all immunized and challenged mock-treated animals produced antibody. The data are consistent with the hypothesis that anti-mu treatment has little effect on multiple cellular immune functions, including those specific for C. albicans, and the combination of antibody, cell-mediated immunity and innate defenses are responsible for solid systemic defense against the fungus.
Desk top video conferencing-an important feature of future visual communications (1990)

The use of the video telephone, normally restricted to two parties, can be extended by including desk top video conferencing facilities. Employing such facilities from conference rooms or studios tends to restrict spontaneity in their use. It is pointed out that this is not the case when a feature of this type is available in the workplace. A multifunctional terminal suitable for such purpose is demonstrated. A solution that makes provision for a conference server for editing sound and picture signals at the switch is presented. For broadband technology, implementation options are described for the video unit, and for narrowband technology, the particular problems involved are pointed out.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Down-regulation of Tumor Necrosis Factor α Expression by Activating Transcription Factor 2 Increases UVC-induced Apoptosis of Late-stage Melanoma Cells (1999)

To identify mechanisms whereby activating transcription factor 2 (ATF2) alters the radiation resistance of human melanoma cells, we examined the possible role of ATF2 in UVC-induced apoptosis. Forced expression of full-length or truncated (Delta1-195 amino acids) forms of ATF2 in LU1205, a late-stage human melanoma cell line, elevated the levels of UVC-induced apoptosis. At the same time, either truncated or full-length forms of ATF2 reduced UVC-induced activation of the tumor necrosis factor-alpha (TNFalpha) promoter and decreased expression of TNFalpha. Forced expression of c-Jun in ATF2-expressing melanoma cells restored TNFalpha expression, suggesting that both forms of ATF2 sequestered transcription factors that positively regulate TNFalpha expression in response to UV irradiation. Antagonistic antibodies to Fas, but not to TNFR1, efficiently suppressed UVC-induced apoptosis, suggesting that the Fas pathway mediates the primary apoptotic signal in melanoma cells whereas the TNFR1 pathway elicits a survival signal. Indeed, treatment of melanoma cells with TNFalpha before UVC irradiation partially suppressed UVC-induced apoptosis, further supporting the protective role of TNFalpha in UVC-treated melanoma cells. Taken together, our findings suggest that ATF2 contributes to UVC-induced apoptosis through transcriptional silencing of TNFalpha, which balances Fas-mediated cell death in melanoma.
Tumstatin, an Endothelial Cell-Specific Inhibitor of Protein Synthesis (2002)

Tumstatin is a 28-kilodalton fragment of type IV collagen that displays both anti-angiogenic and proapoptotic activity. Here we show that tumstatin functions as an endothelial cell-specific inhibitor of protein synthesis. Through a requisite interaction with alphaVbeta3 integrin, tumstatin inhibits activation of focal adhesion kinase (FAK), phosphatidylinositol 3-kinase (PI3-kinase), protein kinase B (PKB/Akt), and mammalian target of rapamycin (mTOR), and it prevents the dissociation of eukaryotic initiation factor 4E protein (eIF4E) from 4E-binding protein 1. These results establish a role for integrins in mediating cell-specific inhibition of cap-dependent protein synthesis and suggest a potential mechanism for tumstatin's selective effects on endothelial cells.
The importance of phase measurement in electrical impedance tomography (1987)

A method is described for reconstructing images of electrical conductivity and relative permittivity in electrical impedance tomography (applied potential tomography). The method relies on measurement of both the amplitude and the phase of the surface electric potential profile. The principle is demonstrated using a computer model to simulate measurements. The reconstructed images, referenced to homogeneous saline, agree qualitatively with the values of conductivity and permittivity used in the computer model. In addition, by displaying the imaginary part of the logarithm of the complex electrical conductivity, certain tissues, e.g. liver and kidney, are emphasised on the image. When the same parameter is displayed for simulated dual-frequency measurements, in which 150 kHz values are referenced against 100 kHz, liver and pancreas are emphasised. These results suggest the possibility of distinguishing between different types of soft tissue more effectively than if only signal amplitudes are measured. The phase changes in the simulated signals, on which the formation of such images depends, have a mean value of 13.3 degrees for the saline-referenced simulation but only 1.6 degrees for the dual-frequency simulation requiring accurate measurement in practice.
Controlled Release of Stromal Cell–Derived Factor-1alpha In Situ Increases C-kit + Cell Homing to the Infarcted Heart (2007)

Stromal-derived factor 1alpha (SDF-1alpha) is a key stem cell homing factor that is crucial for mobilization of stem cells from bone marrow to peripheral blood and subsequent engraftment to the tissue of diseased organs. It has been reported that SDF-1alpha is transiently over-expressed in ischemic myocardium. Therefore, there may be a limited time window after acute myocardial infarction (AMI) during which stem cells are recruited to injured myocardium for repair. This study aimed at investigating whether controlled release of SDF-1alpha via a novel conjugated poly(ethylene glycol) (PEG) (PEGylated) fibrin patch at the infarct site would increase the rate of stem cell recruitment and offer potential therapeutic benefits. Recombinant mouse SDF-1alpha was covalently bound to the PEGylated fibrinogen as evidenced by immunoprecipitation and western blotting. The PEGylated fibrinogen, bound with recombinant mouse SDF-1alpha, was mixed with thrombin to form the PEGylated fibrin patch. The release kinetics of SDF-1alpha were detected in vitro using enzyme-linked immunosorbent assay. Using a mouse AMI model produced by a ligature on the left anterior descending coronary artery, a PEGylated fibrin patch bound with SDF-1alpha (100 ng) was placed on the surface of the infarct area of the left ventricle. Infarct size, left ventricular (LV) function, and the percentage of sca-1(+)/c-kit(+) cells within the infarct area were measured at days 7, 14, and 28 after AMI. In vitro results showed that SDF-1alpha was successfully bound to the PEGylated fibrin patch and can be released from the patch constantly for up to 10 days. Two weeks after infarction, the myocardial recruitment of c-kit(+) cells was significantly higher in the group treated with the SDF-1alpha PEGylated fibrin patch (n = 9) than in the AMI control group (n = 10) (p < 0.05; 11.20 +/- 1.71% vs. 4.22 +/- 0.96%, respectively). At day 28 post-AMI, unlike the control group, the group with the SDF-1alpha-releasing patch maintained stable release of SDF-1alpha concurrent with additional stem cell homing. Moreover, LV function was significantly better than in the control group. These data demonstrate that the PEGylated fibrin patch based SDF-1alpha delivery can improve the rate of c-kit(+) cell homing and improve LV function in hearts with postinfarction LV remodeling.