gebhart/patrepeval huggingface dataset:
Isolation and properties of an extracellular beta-glucosidase from the polycentric rumen fungus Orpinomyces sp. strain PC-2 (1994)

An extracellular beta-glucosidase (EC 3.2.1.21) was purified from culture filtrate of the anaerobic rumen fungus Orpinomyces sp. strain PC-2 grown on 0.3% (wt vol-1) Avicel by using Q Sepharose anion-exchange chromatography, ammonium sulfate precipitation, chromatofocusing ion-exchange chromatography, and Superose 12 gel filtration. The enzyme is monomeric with a M(r) of 85,400, as estimated by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, has a pI of 3.95, and contains about 8.5% (wt vol-1) carbohydrate. The N terminus appears to be blocked. The enzyme catalyzes the hydrolysis of cellobiose and p-nitrophenyl-beta-D-glucoside (PNPG). The Km and Vmax values with cellobiose as the substrate at pH 6.0 and 40 degrees C are 0.25 mM and 27.1 mumol.min-1 x mg-1, respectively; with PNPG as the substrate, the corresponding values are of 0.35 mM and 27.7 mumol.min-1 x mg-1. Glucose (Ki = 8.75 mM, with PNPG as the substrate) and gluconolactone (Ki = 1.68 x 10(-2) and 2.57 mM, with PNPG and cellobiose as the substrates, respectively) are competitive inhibitors. Optimal activity with PNPG and cellobiose as the substrates is at pH 6.2 and 50 degrees C. The enzyme has high activity against sophorose (beta-1,2-glucobiose) and laminaribiose (beta-1,3-glucobiose) but has no activity against gentiobiose (beta-1,6-glucobiose). The activity of the beta-glucosidase is stimulated by Mg2+, Mn2+, Co2+, and Ni2+ and inhibited by Ag+, Fe2+, Cu2+, Hg2+, SDS, and p-chloromercuribenzoate.
Isolation of improved free fatty acid overproducing strains of Escherichia coli via nile red based high‐throughput screening (2011)

Biological production of hydrocarbons is an attractive strategy to produce drop-in replacement transportation fuels. Several methods for converting microbially-produced fatty acids into reduced compounds compatible with petrodiesel have been reported. For these processes to become economically viable, microorganisms must be engineered to approach the theoretical yield of fatty acid products from renewable feedstocks such as glucose. Strains with increased titers can be obtained through both rational and random approaches. While powerful, random approaches require a genetic selection or facile screen that is amenable to high throughput platforms. Here, we present the use of a high throughput screen for fatty acids based on the hydrophobic dye Nile red. The method was applied to screening a transposon library of a free fatty acid overproducing strain of <i>Escherichia coli</i> in search of high producing mutants. Ten gene targets were identified via primary and secondary screening. A strain comprising a clean knockout of one of the identified genes led to a 20% increase in titer over the baseline strain. A selection strategy that combines these findings and can act in an iterative fashion has been developed and can be used for future strain optimization in hydrocarbon producing strains.
Analysis of a human tumor-associated glycoprotein (TAG-72) identified by monoclonal antibody B72.3. (1986)

Monoclonal antibody B72.3 binds a high-molecular-weight tumor-associated glycoprotein identified as TAG-72. This study reports the partial purification and characterization of TAG-72 from a xenograft of a human carcinoma cell line, LS-174T, which expresses high levels of this antigen. The tumor homogenate was initially fractionated by Sepharose CL-4B chromatography. The high-molecular-weight TAG-72, found in the exclusion volume, was then subjected to two sequential passages through B72.3 antibody affinity columns. At each step of the procedure, TAG-72 content was quantitated using a competition radioimmunoassay, and the degree of purification was expressed as the ratio of antigen in units to total protein. The three-step procedure produced a purification of TAG-72 with minimal contamination by other proteins as shown by polyacrylamide gel electrophoresis, followed by staining with Coomassie Blue or periodic acid/Schiff reagent. The density of affinity-purified TAG-72, as determined by cesium chloride gradient ultracentrifugation, was found to be 1.45 g/ml. This density determination, together with the high molecular weight of TAG-72, its resistance to Chondroitinase digestion, the presence of blood group-related oligosaccharides, and sensitivity to shearing into lower-molecular-weight forms suggest that TAG-72 is a mucin-like molecule.
Classification of human emotion from EEG using discrete wavelet transform (2010)

In this paper, we summarize the human emotion recognition using different set of electroencephalogram (EEG) channels using discrete wavelet transform. An audio-visual induction based protocol has been designed with more dynamic emotional content for inducing discrete emotions (disgust, happy, surprise, fear and neutral). EEG signals are collected using 64 electrodes from 20 subjects and are placed over the entire scalp using International 10-10 system. The raw EEG signals are preprocessed using Surface Laplacian (SL) filtering method and decomposed into three different frequency bands (alpha, beta and gamma) using Discrete Wavelet Transform (DWT). We have used “db4” wavelet function for deriving a set of conventional and modified energy based features from the EEG signals for classifying emotions. Two simple pattern classification methods, K Nearest Neighbor (KNN) and Linear Discriminant Analysis (LDA) methods are used and their performances are compared for emotional states classification. The experimental results indicate that, one of the proposed features (ALREE) gives the maximum average classification rate of 83.26% using KNN and 75.21% using LDA compared to those of conventional features. Finally, we present the average classification rate and subsets of emotions classification rate of these two different classifiers for justifying the performance of our emotion recognition system.
CELL-SELEX: Novel Perspectives of Aptamer-Based Therapeutics (2008)

Aptamers, single stranded DNA or RNA molecules, generated by a method called SELEX (systematic evolution of ligands by exponential enrichment) have been widely used in various biomedical applications. The newly developed Cell-SELEX (cell based-SELEX) targeting whole living cells has raised great expectations for cancer biology, -therapy and regenerative medicine. Combining nanobiotechnology with aptamers, this technology opens the way to more sophisticated applications in molecular diagnosis. This paper gives a review of recent developments in SELEX technologies and new applications of aptamers.
Nickel(II) and cobalt(II) complexes of potentially quinquedentate macrobicyclic ligands. Reversible binding of dioxygen to a cobalt(II) complex (1993)

Two new macrobicyclic ligands which are potentially quinquedentate have been prepared and characterised. Variable-temperature NMR studies show that the nickel(II) complex of one of these ligands exists as a mixture of two conformers at low temperature which take part in two independent exchange processes as the temperature is raised. In the first, one conformer undergoes a form of self exchange and in the second, the two conformers interconvert. The ESR spectrum of the cobalt(II) complex of one of the new ligands indicates that it exists as a mixture of four- and five-co-ordinate species, with the five-co-ordinate material arising from intermolecular binding of the ligand secondary amine group to the cobalt(II) ion. This complex binds dioxygen reversibly and the O2 adduct has reasonable stability with respect to autoxidation.
Gene Delivery to Muscle (2001)

The delivery of genes to skeletal muscle by myoblast implantation, DNA injection, or viral transduction has therapeutic applications for human neuromuscular and systemic disorders, many of which are now represented by transgenic or "knockout" mouse models. This unit describes the isolation and retroviral transduction of mouse myoblasts, the injection of myoblasts and plasmid DNA into mouse muscle, and histological methods for analyzing the recipient muscle. A procedure describing the injection of plasmid DNA into muscle with or without electric charge is also included.
The Modelling, Prediction, and Experimental Evaluation of Gear Pump Meshing Pressures with Particular Reference to Aero-Engine Fuel Pumps (2006)

This paper presents the development of a model for the evaluation of pressure transients occurring within an involute tooth form twin-pinion gear pump and addresses, in particular, the influence of cavitation. The latter can cause erosion, limiting the life of such pumps, and liberate hard particles, leading to secondary damage elsewhere. The model considers the inter-tooth volumes that are formed at the roots of the driver and driven gears and utilizes the continuity equations by considering compressible flow into and out of these volumes. Cavitation arising from insufficient flow into the expanding inter-tooth volumes is taken into account. The continuity equations are expressed in terms of fluid density rather than pressure. Hence correct solutions are ensured even during cavitating conditions, when the minimum void pressure is fixed at the appropriate vapour pressure. The effectiveness of the model is assessed through gear pump meshing pressure measurement and flow visualization. The significant influence of inlet pressure ripple on low-pressure predictions is also investigated.
Moving Biomarkers toward Clinical Implementation in Kidney Transplantation (2017)

Long-term kidney transplant outcomes remain suboptimal, delineating an unmet medical need. Although current immunosuppressive therapy in kidney transplant recipients is effective, dosing is conventionally adjusted empirically on the basis of time after transplant or altered in response to detection of kidney dysfunction, histologic evidence of allograft damage, or infection. Such strategies tend to detect allograft rejection after significant injury has already occurred, fail to detect chronic subclinical inflammation that can negatively affect graft survival, and ignore specific risks and immune mechanisms that differentially contribute to allograft damage among transplant recipients. Assays and biomarkers that reliably quantify and/or predict the risk of allograft injury have the potential to overcome these deficits and thereby, aid clinicians in optimizing immunosuppressive regimens. Herein, we review the data on candidate biomarkers that we contend have the highest potential to become clinically useful surrogates in kidney transplant recipients, including functional T cell assays, urinary gene and protein assays, peripheral blood cell gene expression profiles, and allograft gene expression profiles. We identify barriers to clinical biomarker adoption in the transplant field and suggest strategies for moving biomarker-based individualization of transplant care from a research hypothesis to clinical implementation.
p53 Stimulates Promoter Activity of the sgk Serum/Glucocorticoid-inducible Serine/Threonine Protein Kinase Gene in Rodent Mammary Epithelial Cells (1996)

sgk is a novel member of the serine/threonine protein kinase gene family that is transcriptionally regulated by serum and glucocorticoids in mammary epithelial cells. To functionally determine if the sgk promoter is regulated by the p53 tumor suppressor protein in mammary cells, a series of sgk promoter fragments with 5'-deletions were linked to the bacterial chloramphenicol acetyltransferase gene (sgk-CAT) and transiently co-transfected into nontumorigenic NMuMG or transformed Con8Hd6 mammary epithelial cells with p53 expression plasmids. Wild-type p53, but not mutant p53, strongly stimulated sgk promoter activity in both mammary epithelial cell lines. These effects were mediated by specific regions within the sgk promoter containing p53 DNA-binding sites. The sgk p53 sequence at-1380 to-1345 (site IV) was sufficient to confer p53-dependent transactivation to a heterologous promoter, and p53 was capable of binding to this sequence in vitro as assessed by gel shift analysis. In the nontumorigenic NMuMG epithelial cell line, cotransfection of wild-type p53 strongly stimulated the activities of both the sgk promoter and the well characterized p53-responsive p21/Waf1 promoter, whereas in Rat-2 fibroblasts, wild-type p53 repressed the basal activities of both promoters, revealing that sgk and p21/Waf1 are similarly regulated in a cell type-specific manner. Taken together, these results demonstrate that sgk is a new transcriptional target of p53 in mammary epithelial cells and represent the first example of a hormone-regulated protein kinase gene with a functionally defined p53 promoter recognition element.
Wide-field two-dimensional multifocal optical-resolution photoacoustic-computed microscopy (2013)

Optical-resolution photoacoustic microscopy (OR-PAM) is an emerging technique that directly images optical absorption in tissue at high spatial resolution. To date, the majority of OR-PAM systems are based on single-focused optical excitation and ultrasonic detection, limiting the wide-field imaging speed. While 1D multifocal OR-PAM (1D-MFOR-PAM) has been developed, the potential of microlens and transducer arrays has not been fully realized. Here we present the development of 2D multifocal optical-resolution photoacoustic-computed microscopy (2D-MFOR-PACM), using a 2D microlens array and a full-ring ultrasonic transducer array. The 10 mm×10 mm microlens array generates 1800 optical foci within the focal plane of the 512-element transducer array, and raster scanning the microlens array yields optical-resolution photoacoustic images. The system has improved the in-plane resolution of a full-ring transducer array from ≥100 to 29 μm and achieved an imaging time of 36 s over a 10 mm×10 mm field of view. In comparison, the 1D-MFOR-PAM would take more than 4 min to image over the same field of view. The imaging capability of the system was demonstrated on phantoms and animals both ex vivo and in vivo.
Effects of nonionic detergents on P-glycoprotein drug binding and reversal of multidrug resistance. (1993)

Multidrug-resistant cells are thought to maintain low intracellular cytotoxic drug concentration though the active efflux of drugs across the cell membrane. It is presently believed that P-glycoprotein mediates this energy-dependent drug efflux by interacting directly with various lipophilic compounds. In this report, we have used [3H]azidopine in a photoaffinity labeling assay to study the effect of detergents and denaturing agents on P-glycoprotein drug binding in intact cells. Nonionic detergents such as Triton X-100 or Nonidet P-40 at very low concentrations were found to completely abolish azidopine photolabeling to P-glycoprotein and are able to reverse the multidrug resistance phenotype. In contrast, high concentrations of the denaturing agent urea or the zwitterionic detergent 1-[(3-cholamidopropyl)dimethylamino]-1-propanesulfonate did not inhibit azidopine photolabeling to P-glycoprotein. A comparison between verapamil and Triton X-100 revealed that the latter was more effective in inhibiting azidopine photolabeling to P-glycoprotein while verapamil was more effective in potentiating [3H]vinblastine accumulation in drug-resistant cells. Drug transport studies showed that [3H]Triton X-100 accumulated in both drug-sensitive and -resistant cells, and its accumulation was not modulated by excess vinblastine, verapamil, or colchicine. Taken together, these findings suggest that low concentrations of Triton X-100 reverse the multidrug resistance phenotype by inhibiting P-glycoprotein drug binding. In addition, it is also suggested that the site(s) of P-glycoprotein drug binding is localized to sequences found within the lipid bilayer.
Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling (2002)

The search for new TB drugs that rapidly and effectively sterilize the tissues and are thus able to shorten the duration of chemotherapy from the current 6 months has been hampered by a lack of understanding of the metabolism of the bacterium when in a 'persistent' or latent form. Little is known about the condition in which the bacilli survive, although laboratory models have shown that Mycobacterium tuberculosis can exist in a non-growing, drug-resistant state that may mimic persistence in vivo. Using nutrient starvation, we have established a model in which M. tuberculosis arrests growth, decreases its respiration rate and is resistant to isoniazid, rifampicin and metronidazole. We have used microarray and proteome analysis to investigate the response of M. tuberculosis to nutrient starvation. Proteome analysis of 6-week-starved cultures revealed the induction of several proteins. Microarray analysis enabled us to monitor gene expression during adaptation to nutrient starvation and confirmed the changes seen at the protein level. This has provided evidence for slowdown of the transcription apparatus, energy metabolism, lipid biosynthesis and cell division in addition to induction of the stringent response and several other genes that may play a role in maintaining long-term survival within the host. Thus, we have generated a model with which we can search for agents active against persistent M. tuberculosis and revealed a number of potential targets expressed under these conditions.
Immunohistochemical localization of metabotropic glutamate receptors mGluR1a and mGluR2/3 in the rat basal ganglia (1998)

Metabotropic glutamate receptors (mGluRs), which couple glutamate to second messengers, have important roles in the regulation of movement by the basal ganglia. We used two polyclonal antisera to mGluR1a and mGluR2/3 and confocal laser microscopy to investigate the localization of these receptors in the basal ganglia of the rat. The mGluRs were visualized in combination with an antibody to tyrosine hydroxylase (TH), an antibody to microtubule-associated protein 2 (MAP2, a dendritic marker), or SV2 (an antibody to a protein associated with presynaptic terminals). In the neostriatum, punctate mGluR1a immunoreactivity (ir) was present in the neuropil. This staining did not colocalize with MAP2-ir or SV2-ir and was not altered by decortication or unilateral 6-hydroxydopamine (6-OHDA) lesions. In the globus pallidus and substantia nigra pars reticulata, however, mGluR1a-ir was tightly clustered along large MAP2-ir dendrites. In contrast to the variations in mGluR1a-ir staining, similar punctate neuropil mGluR2/3-ir staining was observed within all basal ganglia structures. In the neostriatum, these puncta were abundant; unlike mGluR1a, many mGluR2/3-ir puncta colocalized with SV2-ir, and striatal mGluR2/3-ir puncta were markedly reduced in number after decortication. Neither mGluR1a-ir nor mGluR2/3-ir could be detected in TH-ir soma within substantia nigra pars compacta, or in TH-ir striatal terminals. Overall, our observations suggest that mGluR1a and mGluR2/3 receptors have distinct cellular localizations in different components of the basal ganglia circuitry and are likely to subserve distinct functions. Our data support the presence of mGluR2/3 on the terminals of corticostriatal afferents, where they may regulate glutamate release. In contrast, mGluR1a appears to be a postsynaptic receptor of neurons in the neostriatum, globus pallidus, and substantia nigra pars reticulata.
Eye Movement Patterns in Natural Reading: A Comparison of Monolingual and Bilingual Reading of a Novel (2015)

Bilingual L2 reading patterns show longer sentence reading times (20%), more fixations (21%), shorter saccades (12%) and less word skipping (4.6%), than L1 reading patterns. Regression rates are the same for L1 and L2 reading. These results could indicate, analogous to a previous simulation with the E-Z reader model in the literature, that it is primarily the speeding up of lexical access that drives both L1 and L2 reading development. Bilingual L1 reading does not differ in any major way from monolingual reading. This contrasts with predictions made by the weaker links account, which predicts a bilingual disadvantage in language processing caused by divided exposure between languages.
Studies on the Ecology of Occurrence and Identification of Typhula Snow Mold of Graminous Plants -II. Several Factors Affecting Growth of Typhula incarnata- (1992)

Typhula incarnata grew over a temperature range of -5 to with maximum growth at 10 to . Sclerotial production for T. incarnata was greatest at the higher temperature. Maximum mycelial growth of this pathogen occurred from pH 5.4 to 6.2. When carbon sources were added to a basal salt medium (Czapek's dox agar) at 5 g carbon sources/l, inulin, soluble starch, galactose, glucose, mannose, manitol, sucrose, maltose, cellobirose, trehalose, raffinose, and dextrin supported growth better than other carbon sources did. Of the twenty-three nitrogen sources tested, glycine, serine, ammonium sulfate, asparagine, asparatic acid, and were the most favorable for mycelial growth of T. incarnata. Cystine and cysteine were poor nitrogen sources. Ammonium salt of nitrogen sources supported growth better than nitrate salt of nitrogen sources. Potato dextrose agar, oat meal agar, and V-8 juice agar were the most favorable for mycelial growth and sclerotial formation. Appropriate addition of pepton to PDA decreased mycelial dry weight, but sucrose supported good growth of T. incarnata. Percent viable sclerotia of T. incarnate buried in bentgrass soil decreased from 2 months after treatment remarkably. Trichoderma riride and bacteria were isolated from non-germinated sclerotia. Live orchard grass leaf pieces within the soil were colonized by T. incarnata better than sterile and unsterile dead leaf pieces at . Saprophytic ability of T. incarnate on sterile leaf sheath occurred better at than at . Saprophytic microflora consisting of Cladosporium sp., Fusarium sp., Mucor sp., Pythium sp., and unidentified fungi were the competitors for the sterilized and unsterilized substrate, but their colonization was not find on live leaf sheath buried in the soil at . In the effect of fungicides to Typhula snow mold disease of creeping bentgrass, mixture of polyoxin and thiram was the most effective, followed by iprodione, mixture of iprodione and oxine copper, thiophanate-methyl, myclobutanil, and tolclofos-methyl.
Role of a Putative Polysaccharide Locus in Bordetella Biofilm Development (2006)

Bordetellae are gram-negative bacteria that colonize the respiratory tracts of animals and humans. We and others have recently shown that these bacteria are capable of living as sessile communities known as biofilms on a number of abiotic surfaces. During the biofilm mode of existence, bacteria produce one or more extracellular polymeric substances that function, in part, to hold the cells together and to a surface. There is little information on either the constituents of the biofilm matrix or the genetic basis of biofilm development by Bordetella spp. By utilizing immunoblot assays and by enzymatic hydrolysis using dispersin B (DspB), a glycosyl hydrolase that specifically cleaves the polysaccharide poly-beta-1,6-N-acetyl-D-glucosamine (poly-beta-1,6-GlcNAc), we provide evidence for the production of poly-beta-1,6-GlcNAc by various Bordetella species (Bordetella bronchiseptica, B. pertussis, and B. parapertussis) and its role in their biofilm development. We have investigated the role of a Bordetella locus, here designated bpsABCD, in biofilm formation. The bps (Bordetella polysaccharide) locus is homologous to several bacterial loci that are required for the production of poly-beta-1,6-GlcNAc and have been implicated in bacterial biofilm formation. By utilizing multiple microscopic techniques to analyze biofilm formation under both static and hydrodynamic conditions, we demonstrate that the bps locus, although not essential at the initial stages of biofilm formation, contributes to the stability and the maintenance of the complex architecture of Bordetella biofilms.