gebhart/patrepeval huggingface dataset:
Demonstration of Growth Hormone (GH) Receptor- Associated Tyrosine Kinase Activity in Multiple GHResponsive Cell Types* (1990)

Highly purified GH-receptor preparations from 3T3-F442A fibroblasts, whose differentiation into adipocytes is promoted by GH, have been shown to contain a tyrosine kinase capable of phosphorylating GH receptors. In the current work, characteristics of the tyrosine kinase responsible for the in vitro phosphorylation of GH receptors from cultured 3T3-F442A fibroblasts were examined, and the presence of this GH receptor-associated tyrosine kinase activity was demonstrated in multiple cell types. GH-receptor complexes from GH-treated cells were partially purified by immunoprecipitation using anti-GH antibodies and then incubated as an immune complex with [gamma 32P] ATP. Incorporation of 32P into the GH receptor from 3T3-F442A fibroblasts was apparent within 1 min at 30 C after the addition of [gamma 32P]ATP (5-10 microM). A divalent cation was requisite for the phosphorylation; Mn2+ was significantly more effective than Mg2+ and Co2+; Ba2+, Ca2+, or Zn2+ had no effect. Excess unlabeled ATP, but not cytosine triphosphate, GTP, or uridine triphosphate, abolished 32P incorporation into the GH receptor and [gamma 32P]GTP could not replace [gamma 32P]ATP as a source of 32P. At 5.5 mM Mn2+, phosphorylation exhibited a biphasic dose response to ATP, with maximal phosphorylation occurring at a concentration of 10 microM ATP. At more physiological concentrations of ATP (1 mM), phosphorylation of the GH receptor was also stimulated by lower concentrations of Mn2+ (as low as 500 nM). Optimal reaction conditions determined for the phosphorylation reaction in 3T3-F442A fibroblasts were used to demonstrate incorporation of 32P from [gamma 32P]ATP into partially purified GH receptors from cultured human IM-9 lymphocytes, murine 3T3-F442A adipocytes, rat H-35 hepatoma cells, and freshly isolated rat adipocytes. The 32P was shown to be incorporated into tyrosyl residues in receptors from the two cell types tested (IM-9 lymphocytes and rat adipocytes). Cross-linked [125I] hGH-receptor complexes solubilized from the four cell types (IM-9 lymphocytes, 3T3-F442A adipocytes, H-35 hepatoma cells, and freshly isolated rat adipocytes) bound to and could be eluted from phosphotyrosyl antibody, suggesting that tyrosyl phosphorylation of GH receptors in all of these cells occurs in vivo. The presence of tyrosine kinase activity associated with GH receptors in multiple cell types from different species is consistent with tyrosine kinase activity playing a role in the actions of GH.
Helical-repeat dependence of integrative recombination of bacteriophage lambda: role of the P1 and H1 protein binding sites. (1988)

The efficiency of site-specific recombination of bacteriophage lambda was found to depend on the spacing between distant protein binding sites. Insertions and deletions of up to 30 base pairs were made in the nonessential regions between the H1 and H2 protein binding sites. Recombination was found to occur in substrates with changes of integral multiples of a DNA helical repeat, whereas recombination was defective in substrates with nonintegral changes. The lambda recombinogenic complex is especially interesting because two different proteins are involved: integration host factor (IHF), which has been shown to bend DNA, and the phage-encoded integrase protein (Int), which has been shown to have two distinct DNA-binding domains. The importance of angular displacement of protein binding sites was confirmed by addition of ethidium bromide to defective substrates. Significant stimulation of recombination was observed when sufficient drug intercalated and unwound the DNA to allow improved orientation of sites. The orientation effects are dependent on supercoiling, as spacing is less important in conditions where supercoiling and the P1-H1 sites are not required for recombination.
Audio watermarking for monitoring and copy protection (2000)

Based on existing technology used in image and video watermarking, we have developed a robust audio watermarking technique. The embedding algorithm operates in frequency domain, where the magnitudes of the Fourier coefficients are slightly modified. In the temporal domain, an additional scale parameter and gain function are necessary to refine the watermark and achieve perceptual transparency. Watermark detection relies on the Symmetrical Phase Only Matched Filtering (SPOMF) cross-correlation approach. Not only the presence of a watermark, but also its cyclic shift is detected. This shift supports a multi-bit payload for one particular watermark sequence. The watermarking technology proved to be very robust to a large number of signal processing “attacks” such as MP3 (64 kb/s), all-pass filtering, echo addition, time-scale modification, resampling, noise addition, etc. It is expected that this approach may contribute in a wide variety of existing (e.g. monitoring and copy protection) and future applications.
Cotyledon nuclear proteins bind to DNA fragments harboring regulatory elements of phytohemagglutinin genes. (1989)

The effects of deleting DNA sequences upstream from the phytohemagglutinin-L gene of Phaseolus vulgaris have been examined with respect to the level of gene product produced in the seeds of transgenic tobacco. Our studies indicate that several upstream regions quantitatively modulate expression. Between -1000 and -675, a negative regulatory element reduces expression approximately threefold relative to shorter deletion mutants that do not contain this region. Positive regulatory elements lie between -550 and -125 and, compared with constructs containing only 125 base pairs of upstream sequences (-125), the presence of these two regions can be correlated with a 25-fold and a 200-fold enhancement of phytohemagglutinin-L levels. These experiments were complemented by gel retardation assays, which demonstrated that two of the three regions bind cotyledon nuclear proteins from mid-mature seeds. One of the binding sites maps near a DNA sequence that is highly homologous to protein binding domains located upstream from the soybean seed lectin and Kunitz trypsin inhibitor genes. Competition experiments demonstrated that the upstream regions of a bean beta-phaseolin gene, the soybean seed lectin gene, and an oligonucleotide from the upstream region of the trypsin inhibitor gene can compete differentially for factor binding. We suggest that these legume genes may be regulated in part by evolutionarily conserved protein/DNA interactions.
Analysis of Inter-α-trypsin Inhibitor and a Novel Trypsin Inhibitor, Pre-α-trypsin Inhibitor, from Human Plasma (1989)

The polypeptide chain composition of protein material referred to in the literature as "inter-alpha-trypsin inhibitor" was investigated. The material was found to consist of distinct proteins of 125,000 and 225,000 Da, each of which contained more than one polypeptide chain. The links that assemble each protein were found to be stable to various strong denaturants, but susceptible to treatment with trifluoromethanesulfonic acid or hyaluronidase, indicating a glycan nature. The 225,000-Da protein migrated with inter-alpha mobility on agarose gel electrophoresis and is designated inter-alpha-trypsin inhibitor, whereas the 125,000-Da protein migrated with pre-alpha mobility, and we designate it pre-alpha-trypsin inhibitor. Analysis of the proteins, the separated chains, and proteolytic derivatives thereof revealed that each protein contained a single, identical, trypsin-inhibitory chain of 30,000 Da. Inter-alpha-trypsin inhibitor contains noninhibitory heavy chains of 65,000 and 70,000 Da, whereas pre-alpha-trypsin inhibitor contains a heavy chain of 90,000 Da. Our data allow identification of several recently reported cDNA clones and clarify the confusion surrounding the composition of plasma proteins referred to as inter-alpha-trypsin inhibitor.
Pharmacology of Combination Chemotherapy of Cytosine Arabinoside (Ara-C) and Uracil Arabinoside (Ara-U) or Tetrahydrouridine (THU) against Murine Leukemia L1210/0 in Tumor-Bearing Mice (1987)

Deamination of cytosine arabinoside (ara-C) by cytidine deaminase (Cyt DA) is the main mode of the inactivation of this drug in vivo. Tetrahydrouridine (THU) and the deamination product, uracil arabinoside (ara-U) are potent inhibitors of Cyt DA. We investigated whether ara-U or THU pretreatments can protect ara-C from excessive deamination in tumor- (L1210) bearing mice. In order to determine this, plasma concentrations of ara-C, ara-U, and the intracellular levels of ara-CTP, the active anabolite of ara-C, were assayed. The control peak plasma levels of ara-C and ara-U were 3.3 and 0.78 mM and they were eliminated with a half life (t 1/2) of 1.26 and 1.43 hours, respectively. One hour pretreatment with a nontoxic dose of ara-U (single dose of 300 mg/kg intraperitoneally), resulted in increased ara-C levels by 5.9-fold, while ara-U increased 14.3 fold in comparison with controls. A 24-hour (every 8 hours) pretreatment with ara-U increased ara-C plasma levels by 3.0-fold and it was eliminated with a t 1/2 of 1.21 hours. One hour pretreatment with THU (single dose 25 mg/kg intraperitoneally) enhanced ara-C plasma levels by 5.3-fold. In control L1210/0 acid extracts, ara-CTP peaked at 2 hours and reached 2030 +/- 85 microM; ara-CTP was eliminated with a t 1/2 1.47 hours. The ara-CTP cellular concentrations after 1- and 24-hour pretreatments were 1875 +/- 534 and 2624 +/- 429 microM at 4 hours; the t 1/2 were 2.20 and 1.44 hours, respectively. The THU pretreatment resulted in a peak concentration of ara-CTP of 2208 +/- 366 microM at 2 hours and was eliminated with a t 1/2 of 2.54 hours. We concluded that all pretreatments increased both the peak plasma ara-C concentrations and the area under the plasma concentration-time curve (AUC). One hour ara-U pretreatment did not enhance the peak ara-CTP cellular concentration, but did extend the t 1/2. The 24-hour ara-U and the 1-hour THU pretreatments increased, to some extent, the cellular ara-CTP concentrations, but these differences were not statistically significant. THU pretreatment increased the time the peak occurred and the t 1/2 of ara-CTP. The area under the cellular ara-CTP concentration-time curve (AUC) in L1210 cells was either the same or increased by a small amount after the pretreatments.(ABSTRACT TRUNCATED AT 400 WORDS)
Mechanical properties of dense polylactic acid structures fabricated by three dimensional printing (1997)

Polylactic acid (PLA) is a bioresorbable polymer that is used in a number of clinical situations. Complex shapes of PLA are commonly machined for bone fixation and reconstruction. Solid free from fabrication methods, such as 3D printing, can produce complex-shaped articles directly from a CAD model. This study reports on the mechanical properties of 3D-printed PLLA parts. 3D printing is a solid free-form fabrication process which produces components by ink-jet printing a binder into sequential powder layers. Test bars were fabricated from low and high molecular weight PLA powders with chloroform used as a binder. The binder printed per unit line length of the powder was varied to analyze the effects of printing conditions on mechanical and physical properties of the PLA bars. Furthermore, cold isostatic pressing was performed after printing to improve the mechanical properties of the printed bars. The maximum measured tensile strength for the low molecular weight PLLA (53 000) is 17.40 +/- 0.71 MPa and for high molecular weight PLLA (312 000) is 15.94 +/- 1.50 MPa.
Inhibition of Three Nucleotide Polymerases by Rifamycin Derivatives (1974)

It is possible to design rifamycin derivatives which can distinguish between viral RNA-instructed DNA polymerase and other nucleotide polymerases.
Tau Oligomerization: A Role for Tau Aggregation Intermediates Linked to Neurodegeneration (2008)

Intracellular accumulation of filamentous tau proteins is a defining feature of neurodegenerative diseases, including Alzheimer's disease, progressive supranuclear palsy, corticobasal degeneration, Pick's disease, and frontotemporal dementia with Parkinsonism linked to chromosome 17, all known collectively as tauopathies. Tau protein is a member of microtubule (MT)-associated proteins. Tau is a highly soluble and natively unfolded protein dominated by a random coil structure in solution. It is believed that aberrant modifications of tau, including phosphorylation, truncation, and conformational changes, induce filamentous aggregation. However, the mechanism underlying the conversion of tau protein from a soluble state to one of insoluble aggregates still remains elusive. The importance of tau aggregation intermediates (e.g. tau dimer, tau multimer, and granular tau oligomer) in disease pathogenesis was suggested by recent studies. Here, we review the latest developments in tracking the structural changes of tau protein and discuss the utility improving our understanding of tau aggregation pathway leading to human tauopathies.
Structure of the human MDR3 gene and physical mapping of the human MDR locus. (1991)

Two genes, MDR1 and MDR3, constitute the human P-glycoprotein gene family. To examine the evolutionary relationship between the three known classes of mammalian P-glycoprotein genes, we have cloned the MDR3 gene and compared its structure with that of the human MDR1 and the mouse mdr1 (mdr1b) genes analyzed by other groups. The MDR3 gene contains 28 exons and 27 of these contain coding sequences for the two homologous halves of the protein that correlate with functional domains. This structure is virtually identical to that of the human MDR1 gene and the mouse mdr1 (mdr1b) gene, indicating that the exon/intron structure was fixed before the duplication events that generated different classes of P-glycoproteins, but after the P-glycoproteins diverged from related genes, like the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which has an entirely different exon/intron structure. The four alternatively spliced transcripts of the MDR3 gene arise from alternative splicing of exons 23 and 26. Our analysis of DNA clones covering about 120 kilobases (kb) of the human MDR locus, including the entire MDR3 gene (74 kb) and the intergenic region between both genes (34 kb), combined with pulsed-field gel electrophoresis data shows that the human MDR locus covers about 230 kb. In contrast to the mouse mdr genes, both human genes are transcribed in the same direction (MDR3 located downstream of MDR1). The CpG-rich sequences marking the 5' ends of both genes are hypomethylated to different extents in different cell lines. Hypomethylation roughly correlates with transcriptional activity.
Interfacial Polymerization within a Simplified Microfluidic Device:  Capturing Capsules (2005)

A simple approach to a microfluidic device is described. The device is composed of flexible tubing and a needle inserted orthogonal to the long axis of the tubing. This design is well suited to creating oil-water interfaces allowing the formation of laminar flows and monodisperse emulsions. The system is characterized by mapping the phases observed as a function of organic phase flow and Reynolds number. In addition, the device allows interfacial polymerization reactions to capture low coefficient of variation capsules. The shell structure and surface are examined by scanning electron microscopy.
Targeting Tumour Proliferation with a Small‐Molecule Inhibitor of AICAR Transformylase Homodimerization (2012)

Aminoimidazole carboxamide ribonucleotide transformylase/inosine monophosphate cyclohydrolase (ATIC) is a bifunctional homodimeric enzyme that catalyzes the last two steps of de novo purine biosynthesis. Homodimerization of ATIC, a protein-protein interaction with an interface of over 5000 Å(2), is required for its aminoimidazole carboxamide ribonucleotide (AICAR) transformylase activity, with the active sites forming at the interface of the interacting proteins. Here, we report the development of a small-molecule inhibitor of AICAR transformylase that functions by preventing the homodimerization of ATIC. The compound is derived from a previously reported cyclic hexapeptide inhibitor of AICAR transformylase (with a K(i) of 17 μM), identified by high-throughput screening. The active motif of the cyclic peptide is identified as an arginine-tyrosine dipeptide, a capped analogue of which inhibits AICAR transformylase with a K(i) value of 84 μM. A library of nonnatural analogues of this dipeptide was designed, synthesized, and assayed. The most potent compound inhibits AICAR transformylase with a K(i) value of 685 nM, a 25-fold improvement in activity from the parent cyclic peptide. The potential for this AICAR transformylase inhibitor in cancer therapy was assessed by studying its effect on the proliferation of a model breast cancer cell line. Using a nonradioactive proliferation assay and live cell imaging, a dose-dependent reduction in cell numbers and cell division rates was observed in cells treated with our ATIC dimerization inhibitor.
Buried-oxide silicon-on-insulator structures. I. Optical waveguide characteristics (1992)

For pt.II, see ibid., vol.28, no.1, p.164-75 (1992). Buried-oxide silicon-on-insulator structures are analyzed using both a multilayer transfer matrix approach and a simple approximate method. Results show that these structures can support low-loss leaky modes with substrate leakage losses under 1 dB/cm. Even for a reasonably thick silicon film layer, adjacent modes of the same polarization can have loss discriminations as large as 100 dB/cm. Mode effective indexes obtained from experimental grating transmission measurements taken on waveguides fabricated with the SIMOX process agree with the theoretical analysis.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Transcriptional inhibition of the murine erythropoietin receptor gene by an upstream repetitive element. (1993)

Transcription of the murine erythropoietin receptor (EpoR) gene is inhibited by a novel repetitive element that is located upstream of the EpoR promoter. Reporter gene studies reveal that the inhibitory effect is both distance and orientation dependent. This element is a member of a family of repetitive elements specific to rodents and is present at approximately 10(5) copies per mouse genome. It encodes approximately 500- to 900-bp-long transcripts in both erythroid and nonerythroid cells. RNase protection analysis with a probe from the 5' flanking murine EpoR gene reveals that the direction of transcription is in the sense orientation, relative to the downstream EpoR gene. We suggest that transcriptional inhibition of the EpoR promoter is mediated by read-through transcripts originating in the upstream repetitive element and that this effect may contribute to the basal level of transcription of the murine EpoR gene in erythroid cells.
Human Immunodeficiency Virus Type 1 Vectors with Alphavirus Envelope Glycoproteins Produced from Stable Packaging Cells (2005)

Alphavirus glycoproteins have broad host ranges. Human immunodeficiency virus type 1 (HIV-1) vectors pseudotyped with their glycoproteins could extend the range of tissues that can be transduced in both humans and animal models. Here, we established stable producer cell lines for HIV vectors pseudotyped with alphavirus Ross River virus (RRV) and Semliki Forest virus (SFV) glycoproteins E2E1. RRV E2E1-stable clones could routinely produce high-titer pseudotyped vectors for at least 5 months. SFV E2E1-stable clones, however, produced relatively low titers. We examined the properties of RRV E2E1-pseudotyped vectors [HIV-1(RRV)] and compared them with amphotropic murine leukemia virus Env- and vesicular stomatitis virus glycoprotein G-pseudotyped vectors. HIV-1(RRV) displayed a number of characteristics which would be advantageous in ex vivo and in vivo experiments, including resistance to inactivation by heat-labile components in fresh human sera and thermostability at 37 degrees C. Upon single-step concentration by ultracentrifugation of HIV-1(RRV), we could achieve vector stocks with titers up to 6 x 10(7) IU/ml. HIV-1(RRV) efficiently transduced cells from several different species, including murine primary dendritic cells, but failed to transduce human and murine T cells as well as human hematopoietic stem cells (HSC). These results indicate that HIV-1(RRV) could be used in a number of applications including animal model experiments and suggest that expression of RRV cellular receptors is limited or absent in certain cell types such as T cells and human HSC.
Dynamically composing languages in a modular way: supporting C extensions for dynamic languages (2015)

Many dynamic languages such as Ruby, Python and Perl offer some kind of functionality for writing parts of applications in a lower-level language such as C. These C extension modules are usually written against the API of an interpreter, which provides access to the higher-level language's internal data structures. Alternative implementations of the high-level languages often do not support such C extensions because implementing the same API as in the original implementations is complicated and limits performance. In this paper we describe a novel approach for modular composition of languages that allows dynamic languages to support C extensions through interpretation. We propose a flexible and reusable cross-language mechanism that allows composing multiple language interpreters, which run on the same VM and share the same form of intermediate representation - in this case abstract syntax trees. This mechanism allows us to efficiently exchange runtime data across different interpreters and also enables the dynamic compiler of the host VM to inline and optimize programs across multiple language boundaries. We evaluate our approach by composing a Ruby interpreter with a C interpreter. We run existing Ruby C extensions and show how our system executes combined Ruby and C modules on average over 3x faster than the conventional implementation of Ruby with native C extensions, and on average over 20x faster than an existing alternate Ruby implementation on the JVM (JRuby) calling compiled C extensions through a bridge interface. We demonstrate that cross-language inlining, which is not possible with native code, is performance-critical by showing how speedup is reduced by around 50% when it is disabled.
Effects of Filtration on Glyceraldehyde-3-Phosphate Dehydrogenase mRNA in the Plasma of Trauma Patients and Healthy Individuals (2004)

the purification of the primers, several small peaks appeared, which seem to be extension products coming from n-1 oligonucleotides for the higher molecular weight primers corresponding to the 3958, 3875, and 4446 loci. These peaks were easily identified on all electropherograms.
Stromelysin 3, Ets-1, and Vascular Endothelial Growth Factor Expression in Oral Precancerous and Cancerous Lesions: Correlation with Microvessel Density, Progression, and Prognosis (2005)

In conclusion, this study provides the first evidence of concomitant expression of stromelysin 3, VEGF, and Ets-1 in clinical specimens in different stages of development of oral cancer. In early stages, concomitant expression of stromelysin 3 and Ets-1 favors the development of a precancerous state, whereas dual expression of stromelysin 3 and VEGF is associated with progression from precancerous to cancerous state. VEGF expression is an adverse prognosticator for disease-free survival.