gebhart/patrepeval huggingface dataset:
cDNA and amino acid sequences of the cell adhesion protein receptor recognizing vitronectin reveal a transmembrane domain and homologies with other adhesion protein receptors. (1986)

Cells adhere to vitronectin substrates through a cell surface receptor that recognizes an Arg-Gly-Asp sequence in vitronectin. The receptor is a glycoprotein composed of a 150-kDa alpha and a 115-kDa beta subunit. The alpha subunit consists of two disulfide-bonded chains of 125 kDa and 25 kDa. cDNA clones were isolated for the alpha subunit of the vitronectin receptor from a phage lambda gt11 expression library made with RNA from a human fibroblast cell line, IMR-90. The identity of the clones that had been selected from the library based on immunological criteria was verified by comparison of DNA and protein sequences. NH2-terminal sequences were obtained for each of the alpha-subunit chains. The sequence of the 25-kDa chain of the alpha subunit was found in a cDNA clone, and the amino acid sequence deduced from the cDNA establishes the complete amino acid sequence of the 25-kDa chain. This chain contains a membrane-spanning domain as well as a putative intracytoplasmic region that is 32 amino acids long and consists mostly of polar amino acids. Comparison of the cDNA and protein sequences shows that the 25-kDa chain is generated by proteolytic cleavage of an alpha-subunit precursor, the partial sequence of which is contained in the cDNA clones. These clones contain 1910 base pairs of open reading frame and a 3' untranslated sequence. RNA blot hybridization detected one transcript of about 7 kilobases in RNA from fibroblastic and epithelial cells. Together, the cDNA clones cover 4442 bases of this RNA. The alpha-subunit sequence showed strong homology with the sequence of the alpha subunit of fibronectin receptor. Moreover, the NH2-terminal protein sequence of the 125-kDa chain was homologous with the NH2-terminal sequences of two other cell surface proteins, lymphocyte function-associated antigen 1 (LFA-1) and macrophage antigen 1 (Mac-1), which have been implicated as receptors for adhesion proteins of leukocytes. These results establish several of the structural features in the vitronectin receptor and suggest the existence of a superfamily of receptors for cell adhesion proteins.
Carbon-bonded carbon fiber insulation for radioisotope space power systems (1985)

A carbon-bonded carbon fiber (CBCF) insulation developed for a radioisotope heat source is made from chopped rayon fiber about 10 ..mu..m in diameter and 250 ..mu..m long, which is carbonized and bonded with phenolic resin particles. The CBCF is an excellent lightweight insulating material with a nominal density of 0.2 Mg/m/sup 3/ and a thermal conductivity of 0.24 W/(m-K) in vacuum at 2000/sup 0/C. Several attributes that make CBCF particularly suitable for the heat source application have been identified. These include light weight, low thermal conductivity, chemical compatibility, and high-temperature capabilities. The mechanical strength of CBCF insulation is satisfactory for the application. The basic fabrication technique was refined to eliminate undesirable large pores and cracks often present in materials fabricated by earlier techniques. Also, processing was scaled up to increase the fabrication rate by a factor of 10. The specific properties of the CBCF were tailored by adjusting material and processing variables to obtain the desired results. 22 references, 13 figures, 4 tables.
CDC2L5, a Cdk‐like kinase with RS domain, interacts with the ASF/SF2‐associated protein p32 and affects splicing in vivo (2006)

The human CDC2L5 gene encodes a protein of unknown physiological function. This protein is closely related to the cyclin-dependent kinase (Cdks) family and contains an arginine/serine-rich (RS) domain. The Cdks were first identified as crucial regulators of cell-cycle progression, more recently they were found to be involved in transcription and mRNA processing. RS domains are mainly present in proteins regulating pre-mRNA splicing, suggesting CDC2L5 having a possible role in this process. In this study, we demonstrate that CDC2L5 is located in the nucleoplasm, at a higher concentration in speckles, the storage sites for splicing factors. Furthermore, this localization is dependent on the presence of the N-terminal sequence including the RS domain. Then, we report that CDC2L5 directly interacts with the ASF/SF2-associated protein p32, a protein involved in splicing regulation. Overexpression of CDC2L5 constructs disturbs constitutive splicing and switches alternative splice site selection in vivo. These results argue in favor of a functional role of the CDC2L5 kinase in splicing regulation.
Evaluation of Flagella and Flagellin of Pseudomonas aeruginosa as Vaccines (2009)

Pseudomonas aeruginosa is a serious pathogen in hospitalized, immunocompromised, and cystic fibrosis (CF) patients. P. aeruginosa is motile via a single polar flagellum made of polymerized flagellin proteins differentiated into two major serotypes: a and b. Antibodies to flagella delay onset of infection in CF patients, but whether immunity to polymeric flagella and that to monomeric flagellin are comparable has not been addressed, nor has the question of whether such antibodies might negatively impact Toll-like receptor 5 (TLR5) activation, an important component of innate immunity to P. aeruginosa. We compared immunization with flagella and that with flagellin for in vitro effects on motility, opsonic killing, and protective efficacy using a mouse pneumonia model. Antibodies to flagella were superior to antibodies to flagellin at inhibiting motility, promoting opsonic killing, and mediating protection against P. aeruginosa pneumonia in mice. Protection against the flagellar type strains PAK and PA01 was maximal, but it was only marginal against motile clinical isolates from flagellum-immunized CF patients who nonetheless became colonized with P. aeruginosa. Purified flagellin was a more potent activator of TLR5 than were flagella and also elicited higher TLR5-neutralizing antibodies than did immunization with flagella. Antibody to type a but not type b flagella or flagellin inhibited TLR5 activation by whole bacterial cells. Overall, intact flagella appear to be superior for generating immunity to P. aeruginosa, and flagellin monomers might induce antibodies capable of neutralizing innate immunity due to TLR5 activation, but solid immunity to P. aeruginosa based on flagellar antigens may require additional components beyond type a and type b proteins from prototype strains.
Single-Walled Carbon Nanotubes as a Chemical Sensor for $\hbox{SO}_{2}$ Detection (2007)

Single-walled carbon nanotubes (SWNTs) are Introduced as a chemical sensor for the detection of sulfur dioxide (SO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) molecules. For a single bundle of SWNTs, current-voltage (I-V) curves were measured for a series of different temperatures under adsorption of SO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> molecules. The I-V characteristics for a "MAT"-type thin film SWNTs, with respect to the amount of SO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> adsorbed, were measured at room temperature and compared directly with O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> adsorption. The change in current upon the adsorption of SO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> is distinctly higher than that of O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , and is also reversible for adsorption and successive evacuation. Thus, the results strongly suggested that a thin film of SWNTs can be used as a chemical sensor in the nanometer scale devices.
The role of carbohydrate in recombinant human erythropoietin (1990)

1. Recombinant human erythropoietin has N-linked sugar [Tsuda et al., (1988) Biochemistry 27, 5646-5654]. Here we have demonstrated the presence of O-linked sugar (0.85 mol/mol erythropoietin) composed of sialic acid and Gal beta(1-3)GalNAc. 2. To investigate the role of these sugars, erythropoietins deglycosylated to different extents were prepared using specific glycosidases. Sugars are not essential for in vitro biological activity of erythropoietin, because the fully deglycosylated erythropoietin had the full activity when assayed with in vitro bioassay methods. Asialylation yielded erythropoietin with higher affinity to the receptor than the undigested hormone and therefore an increased in vitro activity. Although erythropoietin from which N-linked or total sugars were removed also had higher affinity for the receptor, their in vitro activity remained unchanged compared with that of the undigested erythropoietin for unknown reasons. On the other hand, removal of sialic acids or N-linked sugar abolished the in vivo biological activity completely, indicating that the presence of N-linked sugar with terminal sialic acids is required for the hormone to reach target sites; full deglycosylation resulted in total loss of the in vivo biological activity of erythropoietin. 3. Incubation of asialo-erythropoietin and fully deglycosylated recombinant human erythropoietin at 70 degrees C for 15 min decreased the biological activity to 35% and 11% of the initial activity, respectively, while the undigested erythropoietin lost no activity. Thus resistance of erythropoietin to thermal inactivation is largely due to the presence of sugars, and terminal sialic acids greatly contribute to the stability.
Classification in the Presence of Label Noise: A Survey (2014)

Label noise is an important issue in classification, with many potential negative consequences. For example, the accuracy of predictions may decrease, whereas the complexity of inferred models and the number of necessary training samples may increase. Many works in the literature have been devoted to the study of label noise and the development of techniques to deal with label noise. However, the field lacks a comprehensive survey on the different types of label noise, their consequences and the algorithms that consider label noise. This paper proposes to fill this gap. First, the definitions and sources of label noise are considered and a taxonomy of the types of label noise is proposed. Second, the potential consequences of label noise are discussed. Third, label noise-robust, label noise cleansing, and label noise-tolerant algorithms are reviewed. For each category of approaches, a short discussion is proposed to help the practitioner to choose the most suitable technique in its own particular field of application. Eventually, the design of experiments is also discussed, what may interest the researchers who would like to test their own algorithms. In this paper, label noise consists of mislabeled instances: no additional information is assumed to be available like e.g., confidences on labels.
Status Epilepticus-Induced Alterations in Metabotropic Glutamate Receptor Expression in Young and Adult Rats (1997)

In adult rats, kainic acid induces status epilepticus and delayed, selective cell loss of pyramidal neurons in the hippocampal CA3. In pup rats, kainate induces status epilepticus but not the accompanying neuronal cell death. The precise mechanisms underlying this age-dependent vulnerability to seizure-induced cell death are not understood. Metabotropic glutamate receptors (mGluRs) are developmentally and spatially regulated throughout the hippocampus and are implicated in seizure-induced damage. In the present study we used in situ hybridization to examine possible changes in mGluR expression at the level of the hippocampus after status epilepticus in postnatal day 10 (P10) pup and adult (P40) rats. Status epilepticus did not alter expression of mGluR1, mGluR3, or mGluR5 mRNAs. In pup and adult rats, status epilepticus induced a reduction in expression of mGluR2 mRNA in granule cells of the dentate gyrus. This change could lead to augmented glutamate release at mossy fiber synapses on CA3 pyramidal cells and thereby promote hyperexcitation. In pup but not adult rats, mGluR4 mRNA expression was enhanced in CA3 pyramidal neurons. Upregulation of presynaptic mGluR4 in pup CA3 neurons could lead to reduced transmitter release from CA3 axons, including recurrent collaterals, thereby reducing vulnerability of neonatal CA3 neurons to seizure-induced damage. These findings indicate that status epilepticus affects mGluR expression in a gene- and cell-specific manner, and that these changes vary with the developmental stage.
The Interdependent Roles of All Players in Making Technology Accessible (2003)

Making technology accessible is a complex and difficult problem, involving many individuals and groups. When a particular technology presents a barrier to an individual, who is at fault? Often blame is assigned to an individual technology developer, content developer, or educational entity, though doing so is often an oversimplification of the problem. In actuality, a variety of players, individually and through relationships with one another, play critical roles in making technology accessible. Players include consumers, technology developers (including developers of assistive technology, operating systems, software applications, user agents, and authoring tools), standards organizations, K-12 and postsecondary schools, employers, advocates and legislators. This article provides an overview of the current state of technology accessibility by examining the roles of each of these players and their interdependencies.
Enhancement-mode InP n-channel metal-oxide-semiconductor field-effect transistors with atomic-layer-deposited Al2O3 dielectrics (2007)

Enhancement-mode (E-mode) n-channel InP metal-oxide-semiconductor field-effect transistors (MOSFETs) with 0.75–40μm gate length fabricated on a semi-insulating substrate with atomic-layer-deposited (ALD) Al2O3 as gate dielectric are demonstrated. The ALD process on III-V compound semiconductors enables the formation of high-quality gate oxides and unpinning of Fermi level on compound semiconductors. A 0.75μm gate length E-mode n-channel MOSFET with an Al2O3 gate oxide thickness of 30nm shows a gate leakage current less than 10μA∕mm at the highest gate bias of 8V, a maximum drain current of 70mA∕mm, and a transconductance of 10mS∕mm. The peak effective mobility is ∼650cm2∕Vs and the interface trap density of Al2O3∕InP is estimated to be ∼(2–3)×1012∕cm2eV.
Extended depth of focus in tomographic phase microscopy using a propagation algorithm (2008)

Tomographic phase microscopy is a laser interferometry technique in which a 3D refractive index map of a biological sample is constructed from quantitative phase images collected at a set of illumination angles. Although the resulting tomographic images provide valuable information, their resolution declines at axial distances beyond about 1 microm from the focal plane. We describe an improved 3D reconstruction algorithm in which the field at the focal plane is numerically propagated to depths throughout the sample. Diffraction is thus incorporated, extending the depth of focus to more than 10 mum. Tomograms with improved focal depth are demonstrated for single HT29 cells.
Suppression of Nerve Growth Factor Trk Receptors and Prolactin Receptors by Endocannabinoids Leads to Inhibition of Human Breast and Prostate Cancer Cell Proliferation1 (2000)

Anandamide and 2-arachidonoylglycerol (2-AG), two endogenous ligands of the CB1 and CB2 cannabinoid receptor subtypes, inhibit the proliferation of PRL-responsive human breast cancer cells (HBCCs) through down-regulation of the long form of the PRL receptor (PRLr). Here we report that 1) anandamide and 2-AG inhibit the nerve growth factor (NGF)-induced proliferation of HBCCs through suppression of the levels of NGF Trk receptors; 2) inhibition of PRLr levels results in inhibition of the proliferation of other PRL-responsive cells, the prostate cancer DU-145 cell line; and 3) CB1-like cannabinoid receptors are expressed in HBCCs and DU-145 cells and mediate the inhibition of cell proliferation and Trk/PRLr expression. Beta-NGF-induced HBCC proliferation was potently inhibited (IC50 = 50-600 nM) by the synthetic cannabinoid HU-210, 2-AG, anandamide, and its metabolically stable analogs, but not by the anandamide congener, palmitoylethanolamide, or the selective agonist of CB2 cannabinoid receptors, BML-190. The effect of anandamide was blocked by the CB1 receptor antagonist, SR141716A, but not by the CB2 receptor antagonist, SR144528. Anandamide and HU-210 exerted a strong inhibition of the levels of NGF Trk receptors as detected by Western immunoblotting; this effect was reversed by SR141716A. When induced by exogenous PRL, the proliferation of prostate DU-145 cells was potently inhibited (IC50 = 100-300 nM) by anandamide, 2-AG, and HU-210. Anandamide also down-regulated the levels of PRLr in DU-145 cells. SR141716A attenuated these two effects of anandamide. HBCCs and DU-145 cells were shown to contain 1) transcripts for CB1 and, to a lesser extent, CB2 cannabinoid receptors, 2) specific binding sites for [3H]SR141716A that could be displaced by anandamide, and 3) a CB1 receptor-immunoreactive protein. These findings suggest that endogenous cannabinoids and CB1 receptor agonists are potential negative effectors of PRL- and NGF-induced biological responses, at least in some cancer cells.
Improving 3D surface reconstruction from endoscopic video via fusion and refined reflectance modeling (2017)

Shape from shading (SFS) has been studied for decades; nevertheless, its overly simple assumptions and its ill-conditioning have resulted in infrequent use in real applications. Price et al. recently developed an iterative scheme named shape from motion and shading (SFMS) that models both shape and reflectance of an unknown surface simultaneously. SFMS produces a fairly accurate, dense 3D reconstruction from each frame of a pharyngeal endoscopic video, albeit with inconsistency between the 3D reconstructions of different frames. We present a comprehensive study of the SFMS scheme and several improvements to it: (1) We integrate a deformable registration method into the iterative scheme and use the fusion of multiple surfaces as a reference surface to guide the next iteration’s reconstruction. This can be interpreted as incorporating regularity of a frame’s reconstruction with that of temporally nearby frames. (2) We show that the reflectance model estimation is crucial and very sensitive to noise in the data. Moreover, even when the surface reflection is not assumed to be Lambertian, the reflectance model estimation function in SFMS is still overly simple for endoscopy of human tissue. By removing outlier pixels, by preventing unrealistic BRDF estimation, and by reducing the falloff speed of illumination in SFS to account for the effect of multiple bouncing of the light, we improve the reconstruction accuracy.
Asenapine Safety, Tolerability, and Pharmacokinetics After Single and Multiple Doses in Healthy Volunteers (2012)

This double-blind, placebo-controlled, randomized study is the first in healthy volunteers to describe the safety, tolerability, and pharmacokinetics of sublingual asenapine at therapeutic dosages. After a 2-day placebo run-in phase, healthy male volunteers received placebo or asenapine escalated to dosages of 3, 5, 10, or 15 mg bid. Another group received single doses (2 and 5 mg) 1 week apart. Serial blood samples were obtained for pharmacokinetic analysis. The single asenapine doses and multiple bid doses up to 10 mg were well tolerated. The most frequent treatment-emergent adverse events were somnolence, oral paresthesia, fatigue, headache, dizziness, and dyspnea. Clinically relevant abnormalities or trends in laboratory and vital signs measures, physical examinations, or electrocardiograms were not observed. Asenapine was rapidly absorbed, with a tmax of ∼1 hour, and was biphasically eliminated with a terminal elimination half-life of 20 to 30 hours. In the range of 3 to 10 mg bid, increases in plasma concentrations were less than dose proportional. Asenapine appears to be well tolerated at single doses up to 5 mg and multiple doses up to 10 mg bid and can be administered to healthy volunteers in clinical pharmacology studies using the dosing regimens described.
Identification of Native Atrial G-protein-regulated Inwardly Rectifying K+ (GIRK4) Channel Homomultimers (1998)

G-protein-regulated inwardly rectifying K+ (GIRK) channels play critical inhibitory roles throughout the nervous system, heart, and pancreas. They are believed to be heterotetramers consisting of GIRK1 (Kir3.1) and either GIRK2 (Kir3.2), GIRK3 (Kir3.3), or GIRK4 (Kir3.4) subunits. The GIRK1 subunit is hypothesized to be critical to form GIRK channels with normal channel kinetics based on heterologous expression studies. However, GIRK2 and GIRK3 proteins are present in areas of the brain where no GIRK1 has been detected. Here we demonstrate that GIRK tetramers lacking GIRK1 can be purified from bovine heart atria. We have found that only half of GIRK4 is purified as the GIRK1-GIRK4 heterotetramer, whereas the remaining GIRK4 forms a high molecular weight, SDS-resistant complex that does not contain GIRK1. These GIRK4 complexes, most likely GIRK4 homotetramers, were previously not seen because of their aberrant migration on SDS-polyacrylamide gels. We propose that all of GIRK1 and half of GIRK4 proteins in atria combine to form the heterotetramer IKACh, whereas the remaining GIRK4 forms a novel tetrameric complex. GIRK4 homotetramers form channels with unusual single channel behavior, and their contribution to native currents requires further investigation.
A colorimetric assay of lysogenic induction designed for screening potential carcinogenic and carcinostatic agents (1979)

Simple, rapid colorimetric tests for lysogenic induction (the derepression of a latent bacterial virus) are described. A quantitative test and a more rapid semiquantitative test are based on the assay of the beta-galactosidase synthesized from lacZ gene fused to an operon under lambda repressor control. These biochemical "inductests" are suitable for screening programs designed to detect agents that damage DNA and that are of potential interest in carcinogenesis and cancer chemotherapy.
Recognition and selection of tRNA in translation (2004)

Aminoacyl-tRNA (aa-tRNA) is delivered to the ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. The stepwise movement of aa-tRNA from EF-Tu into the ribosomal A site entails a number of intermediates. The ribosome recognizes aa-tRNA through shape discrimination of the codon-anticodon duplex and regulates the rates of GTP hydrolysis by EF-Tu and aa-tRNA accommodation in the A site by an induced fit mechanism. Recent results of kinetic measurements, ribosome crystallography, single molecule FRET measurements, and cryo-electron microscopy suggest the mechanism of tRNA recognition and selection.
Identification of Differential Gene Expression by High Throughput Analysis (2000)

High throughput analysis of differential gene expression is a powerful tool that can be applied to many areas in molecular cell biology, including differentiation, development, physiology, and pharmacology. In recent years, a variety of techniques have been developed to analyze differential gene expression, including comparative expressed sequence tag sequencing, differential display, representational difference analysis, cDNA or oligonucleotide arrays, and serial analysis of gene expression. This review explains the technologies, their scopes, impact on science, as well as their costs and possible limitations. The application of differential display is presented as a tool to identify genes induced by darkness or yellowing process in rice leaves.