gebhart/patrepeval huggingface dataset:
A functional prepro-alpha-factor gene in Saccharomyces yeasts can contain three, four, or five repeats of the mature pheromone sequence. (1983)

The chromosomal region containing a structural gene for the mating pheromone precursor prepro-alpha-factor was examined in a variety of Saccharomyces yeasts by using a cloned putative prepro-alpha-factor gene of Saccharomyces cerevisiae as the probe. Analysis by restriction endonuclease digestion and Southern blot hybridization indicated that the physical arrangement of this region is highly conserved in all the Saccharomyces species analyzed, but displays length polymorphisms of limited size (50 to 60 base pairs). The observed polymorphisms were shown to be due solely to differences in the number of tandemly arranged spacer peptide/pheromone units within the coding sequence of these genes. Analysis of polyadenylated RNA indicated that these genes specified RNA transcripts and that these RNA molecules could be translated in vitro into prepro-alpha-factor polypeptides immunoprecipitable with anti-alpha-factor antibodies. The sizes of both the mRNAs and the proteins synthesized from them reflected exactly the differences observed in the lengths of the genes. These findings demonstrate conclusively that the putative prepro-alpha-factor DNA cloned from S. cerevisiae, as well as the sequences detected in the other Saccharomyces species, are indeed expressed and functional genes, and suggest that proper proteolytic processing of prepro-alpha-factor is unaffected by the number of pheromone repeats encoded within this precursor protein.
A rapid fluorescence assay for sphingosine-1-phosphate lyase enzyme activity (2007)

Sphingosine-1-phosphate (S1P) lyase (SPL) catalyzes the conversion of S1P to ethanolamine phosphate and hexadecenal. This enzyme plays diverse roles in physiology and disease and, thus, may be useful as a disease marker and/or drug target. Unfortunately, the radioisotope-based assay currently used to quantify SPL activity is suboptimal. We have devised an assay using a commercially available omega(7-nitro-2-1,3-benzoxadiazol-4-yl)-d-erythro (NBD)-labeled fluorescent substrate. Alternatively, we provide a method for synthesis of the substrate from NBD-sphingosine. Enzyme activity is determined by following the formation of NBD-aldehyde product, which is isolated from unreacted substrate by lipid extraction and quantified after separation by HPLC using a C18 column. A fluorescent NBD-C18-sphingosine internal standard is used to control for extraction efficiency. The reaction is linear over 20 min and total protein concentrations of 20-200 mg/l. The sensitivity of the fluorescence assay is comparable to or better than that of the radioactive assay, and SPL levels as low as 8 pmol/mg/min were readily detected. Semicarbazide, a nonspecific SPL inhibitor, reduced SPL activity in vitro by approximately 70% using both standard and fluorescence methods. Product inhibition was not observed using ethanolamine phosphate and a commercially available source of hexadecenal. This method is suitable for quantifying SPL activity in a variety of cell and tissue sources.
Prevention of Postoperative Peritoneal Adhesions (1982)

The appearance and severity of peritoneal adhesions after simple laparotomy and after adhesiolysis were studied in a rabbit model. Adhesions were induced by direct abrasion with latex glove and dry gauze; control rabbits had abrasion only. Study groups had abrasion and treatment with 10% or 25% povidone. Results showed a significant reduction in the number of adhesions and in the severity of adhesions after treatment with povidone. This study supports the further investigation of the efficacy of povidone in preventing postoperative peritoneal adhesions.
Detection of membrane-bound HLA-G translated products with a specific monoclonal antibody. (1995)

A monomorphic anti-HLA-G monoclonal antibody (mAb) was obtained by immunization of HLA-B27/human beta 2-microglobulin double-transgenic mice with transfected murine L cells expressing both HLA-G and human beta 2-microglobulin. This mAb, designated BFL.1, specifically recognizes, by flow cytometry analysis, the immunizing HLA-G-expressing cells, whereas it does not bind to parental untransfected or to HLA-B7- and HLA-A3-transfected L cells, suggesting that it distinguishes between classical HLA-A and -B and nonclassical HLA-G class I molecules. This was further assessed by the absence of BFL.1 reactivity with a number of human cell lines known to express classical HLA class I proteins. In addition, we showed that the BFL.1 mAb also labels HLA-G-naturally-expressing JEG-3 and HLA-G-transfected JAR human choriocarcinoma cell lines as well as a subpopulation of first-trimester placental cytotrophoblast cells. Further biochemical studies were performed by immunoprecipitation of biotinylated membrane lysates: BFL.1, like the monomorphic W6/32 mAb, immunoprecipitated a 39-kDa protein in HLA-G-expressing cell lines, a size corresponding to the predicted full-length HLA-G1 isoform. However, in contrast to W6/32, which immunoprecipitates both classical and nonclassical HLA class I heavy chains, BFL.1 mAb does not recognize the class Ia products. Such a mAb should be a useful tool for analysis of HLA-G protein expression in various normal and pathological human tissues and for determination of the function(s) of translated HLA-G products.
Cationic Liposomes and Polymers for Gene Transfer (1993)

In this article we describe our experience in the last five years on the development of cationic liposomes and polylysine polymers for direct gene transfer in vitro and in vivo. Various cationic lipids have been synthesized and tested for their activities for formulation of transfection active liposomes. Some empirical rules on the structure requirement of the lipid have been obtained. The entry mechanism of DNA/liposome complex into the cells has been studied with liposomes containing lipopolylysine. Endocytosis of the complex followed by escaping from an endocytotic compartment into the cytosol appears to be the major mechanism. One of the cationic liposome formulations, DC-chol: DOPE liposomes, is being used in a clinical trial for cancer gene therapy. These liposomes can also increase the transfection activity of an antibody-polylysine conjugate without diminishing the target specificity of the conjugate.
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project (2010)

We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor-binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.
A distinct type of alcohol dehydrogenase, , complements ethanol fermentation in an -deficient strain of (2004)

In the fission yeast Schizosaccharomyces pombe, only one alcohol dehydrogenase gene, adh1(+), has been identified. To elucidate the influence of adh1(+) on ethanol fermentation, we constructed the adh1 null strain (delta adh1). The delta adh1 cells still produced ethanol and grew fermentatively as the wild-type cells. Both DNA microarray and RT-PCR analysis demonstrated that this ethanol production is caused by the enhanced expression of a Saccharomyces cerevisiae ADH4-like gene product (SPAC5H10.06C named adh4(+)). Since the strain lacking both adh1 and adh4 genes (delta adh1 delta adh4) showed non-fermentative retarded growth, only these two ADHs produce ethanol for fermentative growth. This is the first observation that a S. cerevisiae ADH4-like alcohol dehydrogenase functions in yeast ethanol fermentation.
Integrating advanced functionality in a microfabricated high-throughput fluorescent-activated cell sorter (2003)

The integration of complete analyses systems "on chip" is one of the great potentials of microfabricated devices. In this study we present a new pressure-driven microfabricated fluorescent-activated cell sorter chip with advanced functional integration. Using this sorter, fluorescent latex beads are sorted from chicken red blood cells, achieving substantial enrichments at a sample throughput of 12000 cells s(-1). As a part of the sorter chip, we have developed a monolithically integrated single step coaxial flow compound for hydrodynamic focusing of samples in flow cytometry and cell sorting. The structure is simple, and can easily be microfabricated and integrated with other microfluidic components. We have designed an integrated chamber on the chip for holding and culturing of the sorted cells. By integrating this chamber, the risk of losing cells during cell handling processes is eliminated. Furthermore, we have also developed integrated optics for cell detection. Our new design contributes to the ongoing efforts for building a fully integrated micro cell sorting and analysing system.
Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life? (2010)

The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. In the extant biosphere the reductive pentose phosphate (Calvin-Benson) cycle is the predominant mechanism by which many prokaryotes and all plants fix CO(2) into biomass. However, the fact that five alternative autotrophic pathways exist in prokaryotes is often neglected. This bias may lead to serious misjudgments in models of the global carbon cycle, in hypotheses on the evolution of metabolism, and in interpretations of geological records. Here, I review these alternative pathways that differ fundamentally from the Calvin-Benson cycle. Revealingly, these five alternative pathways pivot on acetyl-coenzyme A, the turntable of metabolism, demanding a gluconeogenic pathway starting from acetyl-coenzyme A and CO(2). It appears that the formation of an activated acetic acid from inorganic carbon represents the initial step toward metabolism. Consequently, biosyntheses likely started from activated acetic acid and gluconeogenesis preceded glycolysis.
Plasma rich in growth factors: preliminary results of use in the preparation of future sites for implants. (1999)

This article presents preliminary clinical evidence of the beneficial effect of the use of plasma rich in growth factors of autologous origin. The plasma is obtained from the individual patient by plasmapheresis. The macroscopic and microscopic results obtained with bone regeneration using this technique, which uses no membrane or barrier, can be observed. The incorporation of these concepts can introduce several advantages, including the enhancement and acceleration of bone regeneration and more rapid and predictable soft tissue healing.
A novel minimally invasive presacral approach and instrumentation technique for anterior L5–S1 intervertebral discectomy and fusion (2006)

This novel technique of interbody distraction and fusion via a truly percutaneous approach corridor allows for circumferential treatment of the lower lumbar segments with minimal risk to the anterior organs and dorsal neural elements.
Genetic modification of cotton seed oil using inverted-repeat gene-silencing techniques (2000)

Inverted-repeat-based gene constructs targeted against two key cotton seed-specific fatty acid desaturase genes, ghSAD-1, encoding stearoylacvl carrier protein delta9-desaturase and ghFAD2-1, encoding microsomal omega-6 desaturase, were transformed into cotton. The expression of ghSAD-1 and ghFAD2-1 in the inverted-repeat orientation resulted in increased levels of stearic and oleic acids, respectively. Interestingly, the content of palmitic acid in both high-stearic and high-oleic lines was substantially reduced. These materials offer the promise of developing cotton seed oil products with greatly improved nutritional appeal to consumers.
Identification of an amino acid sequence from the laminin A chain that stimulates metastasis and collagenase IV production. (1990)

Tumor cells attach, degrade, and migrate through basement membranes as they metastasize. Laminin, a major glycoprotein of basement membranes, promotes the metastatic activity of tumor cells by stimulating the attachment and migration of the cells and their secretion of collagenase IV. We have identified a synthetic peptide of 19 amino acids (Cys-Ser-Arg-Ala-Arg-Lys-Gln-Ala-Ala-Ser-Ile-Lys-Val-Ala-Val-Ser-Ala-Asp -Arg) from the sequence of the A chain of laminin that increases experimental metastases of the lungs by murine melanoma cells. The peptide is active when injected either intravenously or intraperitoneally. The peptide increased collagenase IV activity, a key enzyme in the breakdown of basement membranes, to the same extent as laminin. This peptide represents an active site on laminin for promotion of the metastatic phenotype and generates a probe for studying the regulation of malignant activities.
[Lumbar intraspinal synovial cysts: imaging and treatment by percutaneous injection. Report of thirteen cases]. (2000)

In patients with radiculopathy and facet degenerative changes, intra spinal synovial cysts must be looked for. Facet corticosteroid injection is a useful alternative to surgical removal.
Efficient inductance extraction via windowing (2001)

We propose a new, efficient and accurate localized inductance modeling technique via windowing in a manner that is analogous to localized capacitance extraction. The stability and accuracy of this process is made possible by twice inverting the localized inductance models, and in the process exploiting properties of the magnetostatic interactions as modeled via the susceptance (inverse inductance). Application of these localized double-inverse inductance models to actual IC bus examples demonstrates the significant improvement in simulation efficiency and overall accuracy as compared to alternative methods of approximation and simplification.
Specificity of Bacillus thuringiensis delta-endotoxins is correlated with the presence of high-affinity binding sites in the brush border membrane of target insect midguts. (1988)

Binding studies were performed with two 125I-labeled Bacillus thuringiensis delta-endotoxins on brush border membrane vesicles prepared from the larval midgut of the tobacco hornworm Manduca sexta or the cabbage butterfly Pieris brassicae. One delta-endotoxin, Bt2-protoxin, is a 130-kDa recombinant crystalline protein from B. thuringiensis subsp. berliner. It kills larvae of both insect species. The active Bt2-toxin is a 60-kDa proteolytic fragment of the Bt2-protoxin. It binds saturably and with high affinity to brush border membrane vesicles from the midgut of both species. The other delta-endotoxin, Bt4412-protoxin, is a 136-kDa crystalline protein from B. thuringiensis subsp. thuringiensis, which is highly toxic for P. brassicae, but not for M. sexta larvae. Bt4412-toxin, obtained after proteolytic activation of Bt4412-protoxin, shows high-affinity saturable binding to P. brassicae vesicles but not to M. sexta vesicles. The correlation between toxicity and specific binding is further strengthened by competition studies. Other B. thuringiensis delta-endotoxins active against M. sexta compete for binding of 125I-labeled Bt2-toxin to M. sexta vesicles, whereas toxins active against dipteran or coleopteran larvae do not compete. Bt2-toxin and Bt4412-toxin bind to different sites on P. brassicae vesicles.
Characterization of Monoclonal Antibodies Against the Human Immunodeficiency Virus (HIV) gag Products and Their Use in Monitoring HIV Isolate Variation (1987)

Monoclonal antibodies were raised against the gag proteins of a British isolate of the human immunodeficiency virus (HIV), CBL-1. Seven of the monoclonal antibodies recognized HIV gag-coded proteins of 55,000 mol. wt. (p55) and 24,000 mol. wt. (p24), three recognized p55/p18 and three p18 alone. Cross-competition assays suggested that at least two independent epitopes exist on the p24 cleaved from the p55 precursor, whereas a cluster of closely related epitopes was recognized by the p55/p18 and p18 antibodies. The panel of monoclonal antibodies was then used to compare by immunofluorescence the expression of gag-encoded antigenic determinants on HIV isolates from different geographical locations. Minor changes in epitope expression were observed in isolates from the U.S.A. and Haiti with the most notable changes being detected in isolates from Zaire, Tanzania and Uganda.
Critical Role of Serum Response Factor in Pulmonary Myofibroblast Differentiation Induced by TGF-β (2009)

Transforming growth factor-beta (TGF-beta) is a cytokine implicated in wound healing and in the pathogenesis of pulmonary fibrosis. TGF-beta stimulates myofibroblast differentiation characterized by expression of contractile smooth muscle (SM)-specific proteins such as SM-alpha-actin. In the present study, we examined the role of serum response factor (SRF) in the mechanism of TGF-beta-induced pulmonary myofibroblast differentiation of human lung fibroblasts (HLF). TGF-beta stimulated SM-alpha-actin expression in HLF, which paralleled with a profound induction of SRF expression and activity. Inhibition of SRF by the pharmacologic SRF inhibitor (CCG-1423), or via adenovirus-mediated transduction of SRF short hairpin RNA (shSRF), blocked the expression of both SRF and SM-alpha-actin in response to TGF-beta without affecting Smad-mediated signaling of TGF-beta. However, forced expression of SRF on its own did not promote SM-alpha-actin expression, whereas expression of the constitutively transactivated SRF fusion protein (SRF-VP16) was sufficient to induce SM-alpha-actin expression, suggesting that both expression and transactivation of SRF are important. Activation of protein kinase A (PKA) by forskolin or iloprost resulted in a significant inhibition of SM-alpha-actin expression induced by TGF-beta, and this was associated with inhibition of both SRF expression and activity, but not of Smad-mediated gene transcription. In summary, this is the first direct demonstration that TGF-beta-induced pulmonary myofibroblast differentiation is mediated by SRF, and that inhibition of myofibroblast differentiation by PKA occurs through down-regulation of SRF expression levels and SRF activity, independent of Smad signaling.
Biophysical Investigation of the Iron in Aft1-1up and Gal-YAH1 Saccharomyces cerevisiae (2011)

Aft1p is a major iron regulator in budding yeast Saccharomyces cerevisiae. It indirectly senses cytosolic Fe status and responds by activating or repressing iron regulon genes. Aft1p within the Aft1-1(up) strain has a single amino acid mutation which causes it to constitutively activate iron regulon genes regardless of cellular Fe status. This leads to elevated Fe uptake under both low and high Fe growth conditions. Ferredoxin Yah1p is involved in Fe/S cluster assembly, and Aft1p-targeted iron regulon genes are also upregulated in Yah1p-depleted cells. In this study Mössbauer, EPR, and UV-vis spectroscopies were used to characterize the Fe distribution in Aft1-1(up) and Yah1p-depleted cells. Aft1-1(up) cells grown in low Fe medium contained more Fe than did WT cells. A basal level of Fe in both WT and Aft1-1(up) cells was located in mitochondria, primarily in the form of Fe/S clusters and heme centers. The additional Fe in Aft1-1(up) cells was present as mononuclear HS Fe(III) species. These species are in a nonmitochondrial location, assumed here to be vacuolar. Aft1-1(up) cells grown in high Fe medium contained far more Fe than found in WT cells. The extra Fe was present as HS Fe(III) ions, probably stored in vacuoles, and as Fe(III) phosphate nanoparticles, located in mitochondria. Yah1p-deficent cells also accumulated nanoparticles in their mitochondria, but they did not contain HS Fe(III) species. Results are interpreted by a proposed model involving three homeostatic regulatory systems, including the Aft1 system, a vacuolar iron regulatory system, and a mitochondrial Fe regulatory system.
Semi-Supervised Classification with Graph Convolutional Networks (2016)

We present a scalable approach for semi-supervised learning on graph-structured data that is based on an efficient variant of convolutional neural networks which operate directly on graphs. We motivate the choice of our convolutional architecture via a localized first-order approximation of spectral graph convolutions. Our model scales linearly in the number of graph edges and learns hidden layer representations that encode both local graph structure and features of nodes. In a number of experiments on citation networks and on a knowledge graph dataset we demonstrate that our approach outperforms related methods by a significant margin.
Characterization and Functional Analysis of thepoxBGene, Which Encodes Pyruvate Oxidase inLactobacillus plantarum (2004)

The pyruvate oxidase gene (poxB) from Lactobacillus plantarum Lp80 was cloned and characterized. Northern blot and primer extension analyses revealed that transcription of poxB is monocistronic and under the control of a vegetative promoter. poxB mRNA expression was strongly induced by aeration and was repressed by glucose. Moreover, Northern blotting performed at different stages of growth showed that poxB expression is maximal in the early stationary phase when glucose is exhausted. Primer extension and in vivo footprint analyses revealed that glucose repression of poxB is mediated by CcpA binding to the cre site identified in the promoter region. The functional role of the PoxB enzyme was studied by using gene overexpression and knockout in order to evaluate its implications for acetate production. Constitutive overproduction of PoxB in L. plantarum revealed the predominant role of pyruvate oxidase in the control of acetate production under aerobic conditions. The DeltapoxB mutant strain exhibited a moderate (20 to 25%) decrease in acetate production when it was grown on glucose as the carbon source, and residual pyruvate oxidase activity that was between 20 and 85% of the wild-type activity was observed with glucose limitation (0.2% glucose). In contrast, when the organism was grown on maltose, the poxB mutation resulted in a large (60 to 80%) decrease in acetate production. In agreement with the latter observation, the level of residual pyruvate oxidase activity with maltose limitation (0.2% maltose) was less than 10% of the wild-type level of activity.