gebhart/patrepeval huggingface dataset:
Genotypic Variation in Cytokinin Oxidase from Phaseolus Callus Cultures (1990)

Genotypic variation in cytokinin oxidase has been detected in enzyme preparations from Phaseolus vulgaris L. cv Great Northern and Phaseolus lunatus L. cv Kingston callus cultures. Although cytokinin oxidase preparations from Great Northern and Kingston callus tissues appear to have very similar substrate specificities, the cytokinin oxidase activities from the two callus tissues were found to differ in a number of other properties. The cytokinin oxidase from P. vulgaris cv Great Northern callus tissue exhibited a pH optimum of 6.5 (bisTris) and had a strong affinity for the lectin concanavalin A. The cytokinin oxidase from P. lunatus cv Kingston callus tissue exhibited a pH optimum of 8.4 (Taps) and did not bind to concanavalin A. The two enzymes also differed in position of elution when chromatographed on DEAE-cellulose. Both cytokinin oxidase activities exhibited enhanced activity and lower pH optima in the presence of copper-imidazole complexes, but the optimum copper-imidazole ratio and the magnitude of enhancement differed for the two activities. In both callus tissues, transient increases in the supply of exogenous cytokinins induced increases in cytokinin oxidase activity. The differences in pH optima and in glycosylation (as evidenced by the observed difference in lectin affinity) of the cytokinin oxidases from Great Northern and Kingston callus tissues suggest that the compartmentation of cytokinin oxidase may differ in the two callus tissues. The possibility that enzyme compartmentation and isozyme variation in cytokinin oxidase may play a role in the regulation of cytokinin degradation in plant tissues is discussed in relation to known differences in the rates of cytokinin degradation in Great Northern and Kingston callus tissues.
19F NMR of 2-deoxy-2-fluoro-D-glucose for tumor diagnosis in mice. An NDP-bound hexose analog as a new NMR target for imaging (1997)

A well-known radiopharmaceutical 2-deoxy-2-fluoro-D-glucose widely used for positron emission tomography diagnosis in terms of glucose utilization, was re-evaluated here as a nuclear magnetic resonance pharmaceutical for cancer detection. The uptake and metabolism of FDG in the experimental tumor, MH134, transplanted to the peritoneum of C3H mice as an ascitic tumor was studied extensively by ex vivo 19F NMR. Prolonged retention of FDG and its metabolites over 2 days was confirmed in the tumor cells as well as in the heart. In these tissues, the 6-phosphate of the injected compound was converted reversibly to its epimer 2-deoxy-2-fluoro-D-mannose and further to their NDP bound forms. The metabolites were almost cleared within a day from the other healthy organs where the formation of NDP-2-deoxy-2-fluoro-D-mannose was low. Thus, the 19F NMR signal of NDP-FDM detected 1 day after the FDG injection could be used as a target signal for tumor detection. Through the use of in vivo 19F NMR spectra and 19F chemical shift images, the feasibility of this proposal was demonstrated. It was concluded that FDG-NMR has a potential for tumor diagnosis in animals.
Failure to deactivate the default mode network indicates a possible endophenotype of autism (2012)

This suggests that a failure to deactivate these regions is a functional endophenotype of autism, related to familial risk for the condition shared between individuals with autism and their siblings.
Surgical Technique: Static Intramedullary Nailing of the Femur and Tibia Without Intraoperative Fluoroscopy (2011)

We describe a simple technique for performing static locked intramedullary nailing of the femur and tibia without fluoroscopy. This technique was successful in most cases and is intended for use with any nailing system only when fluoroscopy or specialized systems for nailing without fluoroscopy are not available.
An improved microstrip Sierpinski carpet antenna (2002)

The boundary integral method coupled with the segmentation method have been used for the first time to analyzed Sierpinski carpet antennas of different order. The close agreement between calculated and measured results for resonant frequency and input return loss indicates that this technique can predict the impedance characteristic accurately. A novel double layered stacked microstrip Sierpinski carpet fractal antenna using a photonic bandgap structure is also presented. This proposed antenna has improved the impedance bandwidth five fold compared to an ordinary microstrip fractal antenna and its radiation pattern is improved due to the removal of unwanted radiation caused by the surface wave.
Purification and characterization of dihydropyrimidine dehydrogenase from human liver. (1992)

Although dihydropyrimidine dehydrogenase has been purified to varying degrees from several species, very little is known about the human enzyme. The importance of this enzyme has recently been shown with cancer chemotherapy, particularly in patients with genetic deficiency of this enzyme. In the present study, this enzyme was purified 7800-fold to homogeneity from human liver by introducing several novel methods including chromatofocusing, HPLC gel filtration, reversed-phase HPLC for the enzyme assay. Purified human enzyme has a molecular mass of 210 +/- 5 kDa and appears to be composed of two subunits. The apparent pI is pH 4.6 (+/- 0.2). The human enzyme contains approximately four flavin nucleotide molecules (two each of FAD and FMN) and 33 iron atoms per molecule of enzyme. Kinetic studies with uracil, thymine, 5-fluorouracil, and NADPH were carried out. Amino acid composition and the N-terminal amino acid sequence of this enzyme were reported. A rabbit polyclonal antibody was raised and shown to be specific for the human liver enzyme. In conclusion, in the present manuscript, we report not only a novel procedure for purification of dihydropyrimidine dehydrogenase from human liver but also new data on its properties compared to other species, which will provide a basis for further biochemical and molecular studies of this enzyme.
Suppression of ICE and Apoptosis in Mammary Epithelial Cells by Extracellular Matrix (1995)

Apoptosis (programmed cell death) plays a major role in development and tissue regeneration. Basement membrane extracellular matrix (ECM), but not fibronectin or collagen, was shown to suppress apoptosis of mammary epithelial cells in tissue culture and in vivo. Apoptosis was induced by antibodies to beta 1 integrins or by overexpression of stromelysin-1, which degrades ECM. Expression of interleukin-1 beta converting enzyme (ICE) correlated with the loss of ECM, and inhibitors of ICE activity prevented apoptosis. These results suggest that ECM regulates apoptosis in mammary epithelial cells through an integrin-dependent negative regulation of ICE expression.
Comparison of MRI Alpha Angle Measurement Planes in Femoroacetabular Impingement (2008)

Insufficient femoral head-neck offset is common in femoroacetabular impingement (FAI) and reflected by the alpha angle, a validated measurement for quantifying this anatomic deformity in patients with FAI. We compared the alpha angle determined on magnetic resonance imaging (MRI) oblique axial plane images with the maximal alpha angle value obtained using radial images. The MRIs of 41 subjects with clinically suspected FAI were reviewed and alpha angle measurements were performed on both oblique axial plane images parallel to the long axis of the femoral neck and radial images obtained using the center of the femoral neck as the axis of rotation. The mean oblique axial plane and mean maximal radial alpha angle values were 53.4 degrees and 70.5 degrees, respectively. In 54% of subjects, the alpha angle was less than 55 degrees on the conventional oblique axial plane image but 55 degrees or greater on the radial plane images. Radial images yielded higher alpha angle values than oblique axial images. Patients with clinically suspected FAI may have a substantial contour abnormality that can be underestimated or missed if only oblique axial plane images are reviewed. Radial plane imaging should be considered in the MRI investigation of FAI.
T Cell-Regulated Neutrophilic Inflammation in Autoinflammatory Diseases (2005)

Previous studies of acute generalized exanthematous pustulosis, a peculiar drug hypersensitivity reaction, suggested that CXCL8-producing T cells regulate sterile, polymorphonuclear neutrophil-rich skin inflammations. In this study, we test the hypothesis of whether CXCL8-producing T cells are present in autoinflammatory diseases like pustular psoriasis and Behçet's disease. Immunohistochemistry of normal skin revealed few CD4+ and CD8+ T cells, few CXCL8+ cells, and no neutrophilic infiltration, whereas in acute exacerbations of atopic dermatitis, numerous CD4+ T cells but few CD8+ T cells, neutrophils, or CXCL8+ cells were detected. In contrast, a pronounced infiltration of neutrophils and of predominantly CD4+ T cells was observed in skin biopsies from pustular psoriasis, Behçet's disease, and acute generalized exanthematous pustulosis, with infiltrating T cells strongly positive for CXCL8 and the chemokine receptor CCR6. Skin-derived T cell clones from pustular skin reactions were positive for CCR6 but negative for CCR8 and secreted high amounts of CXCL8 and GM-CSF, often together with IFN-gamma and TNF-alpha after in vitro stimulation. Moreover, some skin-derived T cell clones from Behçet's disease and from pustular psoriasis predominantly produced CXCL8 and GM-CSF, but failed to secrete IL-5 and IFN-gamma. These cells might represent a particular subset as they differ from both Th1 as well as Th2 T cells and are associated with a unique, neutrophil-rich sterile inflammation. Our findings suggest that CXCL8/GM-CSF-producing T cells may orchestrate neutrophil-rich pathologies of chronic autoinflammatory diseases like pustular psoriasis and Behçet's disease.
Prolactin-Releasing Peptide Mediates Cholecystokinin-Induced Satiety in Mice (2006)

We have shown previously that prolactin-releasing peptide (PrRP) plays a role in the regulation of feeding and energy expenditure in rats. We hypothesize that PrRP may have a physiological action through its putative receptor, GPR10, to mediate the central anorexigenic effects of peripheral satiety factors. Here we examine the effects of PrRP and cholecystokinin (CCK) on feeding in mice, including PrRP receptor gene knockout animals (GPR10(-/-)). Intracerebroventricular administration of PrRP (1-4 nmol) inhibited feeding in C57B6/J mice under both fast-induced and nocturnal feeding conditions. In contrast to the observations made in wild-type mice, neither PrRP nor CCK reduced food intake in GRP10(-/-) mice. The reduction in feeding and the release of corticosterone induced by systemic injection of the stressor lipopolysaccharide was similar in both GPR10(+/+) and GPR10(-/-) mice. These findings suggest that PrRP, acting through GPR10, is involved in regulating food intake and may be a key intermediary in the central satiating actions of CCK.
The SPLASH-2 programs (1995)

The SPLASH-2 suite of parallel applications has recently been released to facilitate the study of centralized and distributed shared-address-space multiprocessors. In this context, this paper has two goals. One is to quantitatively characterize the SPLASH-2 programs in terms of fundamental properties and architectural interactions that are important to understand them well. The properties we study include the computational load balance, communication to computation ratio and traffic needs, important working set sizes, and issues related to spatial locality, as well as how these properties scale with problem size and the number of processors. The other, related goal is methodological: to assist people who will use the programs in architectural evaluations to prune the space of application and machine parameters in an informed and meaningful way. For example, by characterizing the working sets of the applications, we describe which operating points in terms of cache size and problem size are representative of realistic situations, which are not, and which re redundant. Using SPLASH-2 as an example, we hope to convey the importance of understanding the interplay of problem size, number of processors, and working sets in designing experiments and interpreting their results.
Role of ATP Production and Uncoupling Protein-2 in the Insulin Secretory Defect Induced by Chronic Exposure to High Glucose or Free Fatty Acids and Effects of Peroxisome Proliferator-Activated Receptor-γ Inhibition (2002)

In rat pancreatic islets chronically exposed to high glucose or high free fatty acid (FFA) levels, glucose-induced insulin release and mitochondrial glucose oxidation are impaired. These abnormalities are associated with high basal ATP levels but a decreased glucose-induced ATP production (Delta of increment over baseline 0.7 +/- 0.5 or 0.5 +/- 0.3 pmol/islet in islets exposed to glucose or FFA vs. 12.0 +/- 0.6 in control islets, n = 3; P < 0.01) and, as a consequence, with an altered ATP/ADP ratio. To investigate further the mechanism of the impaired ATP formation, we measured in rat pancreatic islets glucose-stimulated pyruvate dehydrogenase (PDH) activity, a key enzyme for pyruvate metabolism and for the subsequent glucose oxidation through the Krebs cycle, and also the uncoupling protein-2 (UCP-2) content by Western blot. In islets exposed to high glucose or FFA, glucose-stimulated PDH activity was impaired and UCP-2 was overexpressed. Because UCP-2 expression is modulated by a peroxisome proliferator- activated receptor (PPAR)-dependent pathway, we measured PPAR-gamma contents by Western blot and the effects of a PPAR-gamma antagonist. PPAR-gamma levels were overexpressed in islets cultured with high FFA levels but unaffected in islets exposed to high glucose. In islets exposed to high FFA concentration, a PPAR-gamma antagonist was able to prevent UCP-2 overexpression and to restore insulin secretion and the ATP/ADP ratio. These data indicate that in rat pancreatic islets chronically exposed to high glucose or FFA, glucose-induced impairment of insulin secretion is associated with (and might be due to) altered mitochondrial function, which results in impaired glucose oxidation, overexpression of the UCP-2 protein, and a consequent decrease of ATP production. This alteration in FFA cultured islets is mediated by the PPAR-gamma pathway.
Compound materials for reversible, phase-change optical data storage (1986)

Results of rapid (laser induced) and slow (heating stage induced) crystallization studies on Te1−xGex, 0≤x≤0.6, are reported. The time it takes to laser crystallize varies with x by more than four orders of magnitude. Films with stoichiometric compositions, Te and GeTe, can be crystallized using laser pulses of less than 100 ns duration. Unlike Te, which spontaneously crystallizes at room temperature, GeTe has a crystallization temperature of &amp;gt;150 °C. From these results we argue that, in general, compound materials allow realization of fast-switching, reversible, phase-change optical recording media. Furthermore, this fast-switching capability, from the amorphous to the crystalline state and back, can be attained simultaneously with long term data (amorphous phase) stability, provided the melting temperature of the compound is sufficiently high.
Association of the fyn protein-tyrosine kinase with the T-cell antigen receptor. (1990)

Activation of the T-cell antigen receptor (TCR) results in tyrosine phosphorylation of the TCR zeta chain and other intracellular substrates. Two other T-cell integral membrane proteins, CD4 and CD8, are associated with the protein-tyrosine kinase (PTK), lck. Despite evidence that activation of this enzyme results in TCR-zeta chain phosphorylation, it has not been shown that the TCR activates lck. We have sought evidence that the TCR is associated with a PTK. In this study we use digitonin to solubilize a murine T-cell hybridoma and demonstrate that antibodies binding extracellular but not intracellular domains of the TCR specifically coprecipitate only the fyn PTK and not lck or yes, two other kinases found in these cells. The association of the fyn PTK with the TCR might enable the T cell to independently regulate two PTKs through surface receptors.
Therapeutic intragastric vaccination against Helicobacter pylori in mice eradicates an otherwise chronic infection and confers protection against reinfection (1997)

Chronic infection of the gastroduodenal mucosae by the gram-negative spiral bacterium Helicobacter pylori is responsible for chronic active gastritis, peptic ulcers, and gastric cancers such as adenocarcinoma and low-grade gastric B-cell lymphoma. The success of eradication by antibiotic therapy is being rapidly hampered by the increasing occurrence of antibiotic-resistant strains. An attractive alternative approach to combat this infection is represented by the therapeutic use of vaccines. In the present work, we have exploited the mouse model of persistent infection by mouse-adapted H. pylori strains that we have developed to assess the feasibility of the therapeutic use of vaccines against infection. We report that an otherwise chronic H. pylori infection in mice can be successfully eradicated by intragastric vaccination with H. pylori antigens such as recombinant VacA and CagA, which were administered together with a genetically detoxified mutant of the heat-labile enterotoxin of Escherichia coli (referred to as LTK63), in which the serine in position 63 was replaced by a lysine. Moreover, we show that therapeutic vaccination confers efficacious protection against reinfection. These results represent strong evidence of the feasibility of therapeutic use of VacA- or CagA-based vaccine formulations against H. pylori infection in an animal model and give substantial preclinical support to the application of this kind of approach in human clinical trials.
Permeabilization of baker’s yeast with N-lauroyl sarcosine (2008)

N-Lauroyl sarcosine (LS), a cationic, non-toxic and biodegradable detergent readily permeabilized whole cells of baker's yeast (Saccharomyces cerevisiae). Permeabilization was carried out to increase assayable cellular catalase activity, an enzyme of great physiological and industrial importance, and to release 5'-nucleotides which find food/nutritional applications. The event of permeabilization was concentration, time and temperature dependent. Maximum permeabilization of yeast cells were observed when 1 g wet weight (0.2 g dry wt) of cells were permeabilized with 1.0 ml of 2% LS at 45 degrees C for 15 min. LS-permeabilized cells showed 350-fold increase in catalase activity and the supernatant obtained after permeabilization was rich in 5'-nucleotides. LS-permeabilized baker's yeast cells can be used as a source of biocatalyst and to isolate valuable by-products.
Synergy in Protein Engineering (1996)

Semisynthesis is a chemical technique of protein engineering that provides a valuable complement to directed mutagenesis. It is the method of choice when the structural modification requires, for example, a noncoded amino acid. The process involves specific and limited protein fragmentation, structural manipulation of the target sequence, and subsequent religation of fragments to give the mutant holoprotein. We suggested and demonstrated that mutagenesis and semisynthesis could be used synergistically to achieve protein engineering goals otherwise unobtainable, if mutagenesis was used to shuffle methionine residues in the yeast cytochrome c sequence (Wallace, C. J. A., Guillemette, J. G., Hibiya, Y., and Smith, M. (1991) J. Biol. Chem. 266, 21355-21357). These residues can not only be sites of specific cleavage by CNBr but also of spontaneous peptide bond synthesis between fragments in noncovalent complexes, which greatly facilitates the semisynthetic process. We have now used an informed "methionine scan" of the protein sequence to discover other useful sites and to characterize the factors that promote this extraordinary and convenient autocatalytic religation. Of eight sites canvassed, in a wide range of settings, five efficiently provoked peptide bond synthesis. The principal factor determining efficiency seems to be the hydropathy of the religation site. The mutants created have also provided some new insights on structure-function relationships in the cytochrome.
Native Morphology of Influenza Virions (2012)

Influenza A virus is an enveloped virus with a segmented, single-strand, negative-sense RNA genome. Its virions show spherical or filamentous shapes of about 100 nm in diameter and occasionally irregular morphology, which exemplifies the pleomorphic nature of these virions. Each viral RNA segment forms a ribonucleoprotein complex (RNP), along with an RNA-dependent RNA polymerase complex and multiple copies of nucleoproteins; the RNPs reside in the enveloped virions. Here, we focus on electron microscopic analyses of influenza virions and RNPs. Based on the morphological and structural observations obtained by using electron microscopic techniques, we present a model of the native morphology of the influenza virion.
Direct activation of the apoptosis machinery as a mechanism to target cancer cells (2003)

Apoptosis plays a pivotal role in the cytotoxic activity of most chemotherapeutic drugs, and defects in this pathway provide a basis for drug resistance in many cancers. Thus the ability to restore apoptosis by using small molecules could have important therapeutic implications. Using a cell-free assay to simultaneously target multiple components of the apoptosis pathway, we identified a class of compounds that activate caspases in a cytochrome c-dependent manner and induce apoptosis in whole cells. By reconstituting the apoptosis pathway with purified proteins, we determined that these compounds promote the protein-protein association of Apaf-1 into the functional apoptosome. These compounds exert cytostatic and cytotoxic effects on a variety of cancer cell lines while having little or no activity against the normal cell lines tested. These findings suggest that direct activation of the basic apoptosis machinery may be a viable mechanism to selectively target cancer.
“Pulling” Nanoparticles into Water:  Phase Transfer of Oleic Acid Stabilized Monodisperse Nanoparticles into Aqueous Solutions of α-Cyclodextrin (2003)

This paper describes a general method to drastically improve the dispersity of oleic acid stabilized nanoparticles in aqueous solutions. We use oleic acid stabilized monodisperse nanoparticles of iron oxides and silver as model systems, and have modified the surface properties of these nanoparticles through the formation of an inclusion complex between surface-bound surfactant molecules and α-cyclodextrin (α-CD). After the modification, the nanoparticles of both iron oxide and Ag can transfer from hydrophobic solvents, such as hexane, to α-CD aqueous phase. The efficiency of the phase transfer to the aqueous solutions depends on the initial α-CD concentration. The α-CD/oleic acid complex stabilized nanoparticles can be stable for long periods of time in aqueous phase under ambient atmospheric conditions. Transmission electron microscopy (TEM), ultraviolet−visible (UV−vis) spectroscopy, Fourier transform-infrared (FT-IR) spectroscopy, and colorimetric methods have been used in the characterization of these nanoparticles.