gebhart/patrepeval huggingface dataset:
Structural elements that regulate pp59c-fyn catalytic activity, transforming potential, and ability to associate with polyomavirus middle-T antigen (1991)

Except for its unique amino-terminal region (residues 1 through 83), which possibly dictates substrate recognition, pp59c-fyn bears a high degree of homology with other members of the src family of tyrosine kinases. Here we show that the carboxy terminus of pp59c-fyn is necessary for stable middle-T-antigen association, that pp59c-fyn is normally phosphorylated on both serine and tyrosine residues, and that Tyr-531 and Tyr-420 are phosphorylation sites in vivo and in vitro, respectively. Analysis of a spontaneously generated mutant encoding a truncated form of pp59c-fyn and of variants specifically mutated at the Tyr-531 and Tyr-420 phosphorylation sites indicates that pp59c-fyn has regulatory elements analogous to those that have already been identified for other src-like tyrosine kinases. However, further examination of the pp59c-fyn variants suggests the likelihood of additional means by which its activities might be regulated. Although alteration of Tyr-531 to phenylalanine (531F) in pp59c-fyn results in a protein which is more active enzymatically that the wild type, the enhancement is much less than that for the analogous variant of pp60c-src. Furthermore, contrary to results of similar experiments on other src-like proto-oncogene products, 531F did not induce transformation of NIH 3T3 cells. Studies involving pp59c-fyn-pp60c-src chimeras in which the unique amino-terminal sequences (residues 1 through 83) of the two kinases were precisely interchanged implied that the inability of 531F to induce transformation is probably not caused by the absence of substrates for pp59c-fyn in NIH 3T3 cells but rather by the insufficient enhancement of pp59c-fyn kinase activity. It is therefore probable that the kinase and transforming activities of pp59c-fyn are repressed by additional regulatory elements possibly located in the amino-terminal half of the molecule.
Acute kidney injury in the rat causes cardiac remodelling and increases angiotensin‐converting enzyme 2 expression (2008)

Patients with kidney failure are at high risk of a cardiac death and frequently develop left ventricular hypertrophy (LVH). The mechanisms involved in the cardiac structural changes that occur in kidney failure are yet to be fully delineated. Angiotensin-converting enzyme (ACE) 2 is a newly described enzyme that is expressed in the heart and plays an important role in cardiac function. This study assessed whether ACE2 plays a role in the cardiac remodelling that occurs in experimental acute kidney injury (AKI). Sprague-Dawley rats had sham (control) or subtotal nephrectomy surgery (STNx). Control rats received vehicle (n = 10), and STNx rats received the ACE inhibitor (ACEi) ramipril, 1 mg kg(-1) day(-1) (n = 15) or vehicle (n = 13) orally for 10 days after surgery. Rats with AKI had polyuria (P < 0.001), proteinuria (P < 0.001) and hypertension (P < 0.001). Cardiac structural changes were present and characterized by LVH (P < 0.001), fibrosis (P < 0.001) and increased cardiac brain natriuretic peptide (BNP) mRNA (P < 0.01). These changes occurred in association with a significant increase in cardiac ACE2 gene expression (P < 0.01) and ACE2 activity (P < 0.05). Ramipril decreased blood pressure (P < 0.001), LVH (P < 0.001), fibrosis (P < 0.01) and BNP mRNA (P < 0.01). These changes occurred in association with inhibition of cardiac ACE (P < 0.05) and a reduction in cardiac ACE2 activity (P < 0.01). These data suggest that AKI, even at 10 days, promotes cardiac injury that is characterized by hypertrophy, fibrosis and increased cardiac ACE2. Angiotensin-converting enzyme 2, by promoting the production of the antifibrotic peptide angiotensin(1-7), may have a cardioprotective role in AKI, particularly since amelioration of adverse cardiac effects with ACE inhibition was associated with normalization of cardiac ACE2 activity.
Über Orceinfarbstoffe, XVI. Die Autoxydation von Resorcinderivaten, insbesondere des 4.5‐Dimethyl‐resorcins (1962)

Abstract Die Autoxydationsprodukte von methylsubstituierten Resorcinderivaten zeigen an, daß im Orcein über die bisher isolierten vierzehn Komponenten keine weiteren Phenoxazonfarbstoffe vorkommen. Bei der Autoxydation von 4.5‐Dimethyl‐resorcin in wäßr. Ammoniak entsteht 7‐Hydroxy‐3.4.5.6‐tetramethyl‐phenoxazon‐(2).
Sterically Stabilized pH-sensitive Liposomes, INTRACELLULAR DELIVERY OF AQUEOUS CONTENTS AND PROLONGED CIRCULATION IN VIVO (1997)

Liposomes that destabilize at mildly acidic pH are efficient tools for delivering water-soluble drugs into the cell cytoplasm. However, their use in vivo is limited because of their rapid uptake from circulation by the reticuloendothelial system. Lipid-anchored polyethylene glycol (PEG-PE) prolongs the circulation time of liposomes by steric stabilization. We have found that addition of PEG-PE to the membrane of pH-sensitive liposomes composed of cholesteryl hemisuccinate (CHEMS) and dioleoylphosphatidylethanolamine (DOPE) confers steric stability to these vesicles. This modification significantly decreases the pH-dependent release of a charged water-soluble fluorophore, calcein, from liposomes suspended in buffer or cell culture medium. However, the ability of such liposomes to release calcein intracellularly, measured by a novel flow cytometry technique involving dual fluorescence labeling, remains unaltered. As expected, the release of calcein from liposomes endocytosed by cells is inhibited upon pretreatment of the cells with NH4Cl, an inhibitor of endosome acidification. The unique properties of these liposomes were also demonstrated in vivo. The distribution kinetics of 111In-containing CHEMS/DOPE/PEG-PE liposomes injected intravenously into rats has pharmacokinetic parameters similar to control, non-pH-sensitive, sterically stabilized CHEMS/distearoylphosphatidylcholine/PEG-PE liposomes. In contrast, regular pH-sensitive liposomes lacking the PEG-PE component are cleared rapidly. Sterically stabilized pH-sensitive liposomes may therefore be useful for the intracellular delivery in vivo of highly negatively charged molecules such as genes, antisense oligonucleotides, and ribozymes for the treatment of various diseases.
THE HAU OF THE GIFT IN ITS CULTURAL CONTEXT (1987)

Ethnocentricity is always a problem for the ethnographer. So also is a superficial or too narrow focus on a particular feature. Dealing with secondary sources adds further to the difficulties of reaching a clear view. These handicaps are all involved in the attempt of Marcel Mauss to use a single element of Maori culture, the notion of hau as it is involved in gift exchange, in building a “general theory of obligation” (Mauss 1952:10). He interprets hau of the gift as “spirit” of the gift. In this paper I argue that his isolation of hau and neglect of other cultural factors involved led him to personify hau and credit it with too much importance. Marcel Mauss’s Essay on the Gift has been described as “his own gift to the ages” (Sahlins 1974: 149), a “valuable analysis” (Firth 1959:418), an “influential essay” (MacCormack 1976:97), and the “relapse of Mauss” (Panoff, in McCall 1982:303). Yet it also provoked these writers to dissect Mauss’s interpretation and then attempt to reconstruct the “true” meaning of hau themselves. However, these attempts have been largely reworkings of the same limited data. While dependence on secondary sources is unavoidable in reassessing the meaning of hau, the problems of ethnocentricity, narrow focus, and consequent distorted interpretations can be reduced by placing the discussion in a much broader cultural context. This is the basis of my
Structure and interactions of heparan sulfate proteoglycans from a mouse tumor basement membrane (1984)

Various forms of heparan sulfate proteoglycan were solubilized from the mouse Engelbreth-Holm-Swarm (EHS) sarcoma by extraction with 0.5 M NaCl, collagenase digestion and extraction with 4 M guanidine. They could be separated into high (greater than or equal to 1.65 g/ml) and low (1.38 g/ml) buoyant density variants. The high-density form from the NaCl extract and collagenase digest had Mr = 130000 and So20,W = 4.5 S and contained 4-10% protein, indicating Mr = 5 000-12 000 for the protein core. This proteoglycan exhibited polydispersity as shown by rotary shadowing electron microscopy and ultracentrifugation. An average molecule consisted of four heparan sulfate chains (Mr = 29 000) each with a length of 32 +/- 10 nm. The low-density form (Mr about 400 000) could not be completely purified and contained about 50% protein. As shown by radioimmunoassay, the various proteoglycans shared similar protein cores. Labeling of the tumor in vivo or in vitro demonstrated preferential incorporation of radioactive sulfate in the high-density form. The high-density proteoglycan interacted in affinity chromatography by virtue of its heparan sulfate chains with laminin, fibronectin, the globular domain NC1 and the triple helix of collagen IV. These interactions were abolished at moderate concentrations of NaCl (0.1-0.2 M) and in the presence of heparin, chondroitin sulfate or dextran sulfate. Interactions with the globule NC1 could also be demonstrated by velocity band centrifugation in sucrose gradients and a binding constant of about 10(6) M-1 was derived.
Detection of THCA in Oral Fluid by GC-MS-MS (2006)

A major marijuana metabolite, 11-nor-9-carboxy-tetrahydrocannabinol (THCA), has been identified in oral fluids from donors that previously tested positive for Delta(9)-tetrahydrocannabinol (THC). The method consisted of solid-phase extraction of the oral fluid samples followed by gas chromatography-tandem mass spectrometry analysis of the extracts. Testing for THCA was performed on 223 oral fluid samples previously analyzed for THC. The THCA assay was linear from 10 to 240 pg/mL. The mean recovery of spiked THCA in oral fluid was 104%, and precision was 4% at 20 pg/mL using fortified negative samples. This method was rugged and robust, providing detection and quantification of THCA in oral fluids at levels not previously reported. Results of this study showed that THCA was detectable in 21 of 26 oral fluid samples previously reported positive for THC. The range of concentrations from these samples was from 10 pg/mL up to 142 pg/mL THCA.
Critical Roles of Activation-Induced Cytidine Deaminase in the Homeostasis of Gut Flora (2002)

Activation-induced cytidine deaminase (AID) plays an essential role in class switch recombination (CSR) and somatic hypermutation (SHM) of immunoglobulin genes. We report here that deficiency in AID results in the development of hyperplasia of isolated lymphoid follicles (ILFs) associated with a 100-fold expansion of anaerobic flora in the small intestine. Reduction of bacterial flora by antibiotic treatment of AID-/- mice abolished ILF hyperplasia as well as the germinal center enlargement seen in secondary lymphoid tissues. Because an inability to switch to immunoglobulin A on its own does not lead to a similar phenotype, these results suggest that SHM of ILF B cells plays a critical role in regulating intestinal microflora.
A Virus-Like Particle That Elicits Cross-Reactive Antibodies to the Conserved Stem of Influenza Virus Hemagglutinin (2012)

The discovery of broadly neutralizing antibodies that recognize highly conserved epitopes in the membrane-proximal region of influenza virus hemagglutinin (HA) has revitalized efforts to develop a universal influenza virus vaccine. This effort will likely require novel immunogens that contain these epitopes but lack the variable and immunodominant epitopes located in the globular head of HA. As a first step toward developing such an immunogen, we investigated whether the 20-residue A-helix of the HA2 chain that forms the major component of the epitope of broadly neutralizing antibodies CR6261, F10, and others is sufficient by itself to elicit antibodies with similarly broad antiviral activity. Here, we report the multivalent display of the A-helix on icosahedral virus-like particles (VLPs) derived from the capsid of Flock House virus. Mice immunized with VLPs displaying 180 copies/particle of the A-helix produced antibodies that recognized trimeric HA and the elicited antibodies had binding characteristics similar to those of CR6261 and F10: they recognized multiple HA subtypes from group 1 but not from group 2. However, the anti-A-helix antibodies did not neutralize influenza virus. These results indicate that further engineering of the transplanted peptide is required and that display of additional regions of the epitope may be necessary to achieve protection.
Molecular Mechanisms of Myogenic Coactivation by p300: Direct Interaction with the Activation Domain of MyoD and with the MADS Box of MEF2C (1997)

By searching for molecules that assist MyoD in converting fibroblasts to muscle cells, we have found that p300 and CBP, two related molecules that act as transcriptional adapters, coactivate the myogenic basic-helix-loop-helix (bHLH) proteins. Coactivation by p300 involves novel physical interactions between p300 and the amino-terminal activation domain of MyoD. In particular, disruption of the FYD domain, a group of three amino acids conserved in the activation domains of other myogenic bHLH proteins, drastically diminishes the transactivation potential of MyoD and abolishes both p300-mediated coactivation and the physical interaction between MyoD and p300. Two domains of p300, at its amino and carboxy terminals, independently function to both mediate coactivation and physically interact with MyoD. A truncated segment of p300, unable to bind MyoD, acts as a dominant negative mutation and abrogates both myogenic conversion and transactivation by MyoD, suggesting that endogenous p300 is a required coactivator for MyoD function. The p300 dominant negative peptide forms multimers with intact p300. p300 and CBP serve as coactivators of another class of transcriptional activators critical for myogenesis, myocyte enhancer factor 2 (MEF2). In fact, transactivation mediated by the MEF2C protein is potentiated by the two coactivators, and this phenomenon is associated with the ability of p300 to interact with the MADS domain of MEF2C. Our results suggest that p300 and CBP may positively influence myogenesis by reinforcing the transcriptional autoregulatory loop established between the myogenic bHLH and the MEF2 factors.
Rapid and specific detection of the pap, afa, and sfa adhesin-encoding operons in uropathogenic Escherichia coli strains by polymerase chain reaction (1992)

Adhesin-encoding operons (pap, sfa/foc, and afa) have been shown to be prevalent in Escherichia coli strains associated with urinary tract infections. A quick and sensitive assay to identify these operons was developed by using the polymerase chain reaction (PCR). Three pairs of 25-mer primers were defined from the sequences of the DNA fragments used as probes in hybridization studies to identify each of the three operons, and the six primers were used together in a single reaction of amplification. To validate the PCR approach for detection of adhesin-encoding operons among clinical isolates, we investigated a collection of 97 E. coli isolates with the following characteristics: all isolates originated from the urine of patients with pyelonephritis, and the adhesin responsible for specific binding of the isolates to uroepithelial cells was previously characterized by phenotypic assays, as well as genotypic tests based on hybridization. There was a perfect correlation between the results obtained with the PCR approach and those previously obtained by using DNA probes. These results indicate that the PCR method, which is highly specific and easier to perform than the hybridization method, is a powerful genotypic assay for detection of adhesin-encoding operons. Thus, this assay can be recommended for clinical use to detect virulent urinary E. coli strains, as well as for epidemiological studies.
RNA–protein interactions in the yeast three-hybrid system: Affinity, sensitivity, and enhanced library screening (2004)

The yeast three-hybrid system has become a useful tool in analyzing RNA-protein interactions. An RNA sequence is tested in combination with an RNA-binding protein linked to a transcription activation domain (AD). A productive RNA-protein interaction activates a reporter gene in vivo. The system has been used to test candidate RNA-protein pairs, to isolate mutations in each interacting partner, and to identify proteins that bind a given RNA sequence. However, the relationship between reporter gene activation and in vitro affinity of an RNA-protein interaction has not been examined systematically. This limits interpretation of the data and complicates the development of new strategies. Here, we analyze several key parameters of the three-hybrid system, using as a model the interaction of a PUF protein, FBF-1, with a range of RNA targets. We compare activation of two reporter genes as a function of the in vitro affinity of the interaction. HIS3 and LacZ expression levels are directly related to affinity over a 10-fold range of Kd. Expression of the reporter genes also is directly related to the abundance of the activation domain fusion protein. We describe a new yeast strain, YBZ1, that simplifies screening of cDNA/AD libraries. This strain possesses a tandem, head-to-tail dimer of a high-affinity variant of MS2 coat protein, fused to a monomer of the LexA DNA-binding protein. We show that the use of this strain in cDNA library screens increases the number of genuine, sequence-specific positives detected, and at the same time reduces the background of false, RNA-independent positives.
Expression of catalytically inactive Syp phosphatase in 3T3 cells blocks stimulation of mitogen-activated protein kinase by insulin. (1994)

To explore the role of the protein tyrosine phosphatase Syp in insulin signaling, a catalytically inert mutant Syp protein was expressed under an inducible promoter in cells transfected with the human insulin receptor. Expression of the mutant phosphatase significantly reduced the stimulation of mitogenesis by insulin, indicating that the mutation produced a dominant negative phenotype. Tyrosine phosphorylation of both the insulin receptor and its major substrates, Shc and insulin receptor substrate-1, were unaffected by the mutant phosphatase. However, both the insulin-dependent tyrosine phosphorylation and activation of mitogen-activated protein kinase were markedly attenuated. Expression of the mutant phosphatase allowed the detection of a 120-kDa protein phosphorylated in response to insulin that associated with the src homology (SH) 2 domains of the phosphatase, suggesting a possible regulatory role for this protein. These results indicate that the activity of Syp plays a critical part in the mitogenic actions of insulin.
Heterogeneity of human polymorphonuclear leukocyte receptors for leukotriene B4. Identification of a subset of high affinity receptors that transduce the chemotactic response. (1984)

Human polymorphonuclear (PMN) leukocytes bound [3H]leukotriene B4 ([3H]-LTB4) specifically, as assessed by the displacement of 88% or more of the bound radioactivity by a 15,000-fold higher concentration of nonradioactive LTB4 or by micromolar concentrations of structural isomers of LTB4. The specific binding of [3H]LTB4 by PMN leukocytes was characterized by rapid association and dissociation, and was saturable at 800 nM LTB4. The results of computer analyses of the concentration dependence of binding of [3H]LTB4 were consistent with the expression of two classes of receptors having respective mean affinities of 3.9 X 10(-10) M and 6.1 X 10(-8) M and mean densities of 4.4 X 10(3) and 2.7 X 10(5) per PMN leukocyte. Structural isomers of LTB4 inhibited the binding of [3H]LTB4 to PMN leukocytes at concentrations similar to those required to elicit chemotaxis, while chemotactic peptides did not inhibit binding. PMN leukocytes that were deactivated by prior exposure to LTB4 lost high affinity binding sites selectively and concurrently with a reduction in the chemotactic response to LTB4. Chemotactic deactivation altered, but did not eliminate, the low affinity receptors for LTB4 and reduced only minimally the lysosomal degranulation elicited by LTB4. The high affinity receptors for LTB4 on normal human PMN leukocytes appear to transduce the chemotaxis evoked by LTB4 without substantially modifying lysosomal degranulation.
Reduced beta-catenin expression in the cytoplasm of advanced-stage superficial spreading malignant melanoma. (2003)

In summary, we hypothesize that cytoplasmic beta-catenin has a protective role in early melanoma development.
“Interferometric ground-roll removal: Attenuation of scattered surface waves in single-sensor data,” G EOPHYSICS , 75, no. 2, SA15–SA25. (2010)

Abstract To: “Interferometric ground-roll removal: Attenuation of scattered surface waves in single-sensor data,” David F. Halliday, Andrew Curtis, Peter Vermeer, Claudio Strobbia, Anna Glushchenko, Dirk-Jan van Manen, and Johan O. A. Robertsson, Geophysics, 75, no. 2, SA15–SA25.
Optical Spatially Quantized High Performance Analog-to-digital Conversion (2007)

We present an optical spatial quantized analog-to-digital converter (ADC) and experimentally demonstrate 8-level quantization consuming only 7.2 pJ per quantization operation. Measured 8 ps full-width half-maximum photodetector outputs, promises the potential of realizing a 3 bit 125 GS/s ADC.
Induction and Transcription Studies of the Dextransucrase Gene in Leuconostoc mesenteroides NRRL B-512F (1999)

Dextransucrase production by Leuconostoc mesenteroides NRRL B-512F in media containing carbon sources other than sucrose is reported for the first time. Dextransucrases were analyzed by gel electrophoresis and by an in situ activity assay. Their polymers and acceptor reaction products were also compared by (13)C nuclear magnetic resonance and high-performance liquid chromatography techniques, respectively. From these analyses, it was found that, independently of the carbon source, L. mesenteroides NRRL B-512F produced dextransucrases of the same size and product specificity. The 5' ends of dextransucrase mRNAs isolated from cells grown under different culture conditions were identical. Based on this evidence, we conclude that dextransucrases obtained from cells grown on the various carbon sources result from the transcription of the same gene. The control of expression occurs at this level. The low dextransucrase yields from cultures in D-glucose or D-fructose and the enhancement of dextransucrase gene transcription in the presence of sucrose suggest that an activating phenomenon may be involved in the expression mechanism. Dextransucrase mRNA has a size of approximately 4.8 kb, indicating that the gene is located in a monocistronic operon. The transcription start point was localized 34 bp upstream from the ATG start codon. The -10 and -35 sequences found, TATAAT and TTTACA, were highly homologous to the only glycosyltransferase promoter sequence reported for lactic acid bacteria.
Amorphous silicon dual-mode medical imaging system (1998)

An amorphous silicon medical imaging system designed to operate in both radiographic and fluoroscopic modes is described. Images of medical phantoms are presented for both modes of operation. MTF and DQE measurements are also presented. The effect of recursive filtering on the DQE performance of the system operating in fluoroscopic mode is discussed.