gebhart/patrepeval huggingface dataset:
Molecular context of a viral T cell determinant within a chimeric bacterial protein alters the diversity of its T cell recognition. (1994)

We genetically introduced two different viral CD4+ T cell epitopes within two internal sites of the Escherichia coli maltose-binding (MalE) protein. Affinity-purified hybrid MalE proteins were used to analyze the influence of the molecular environment on the presentation of inserted epitope to T cells. In the first model, the 120 to 132 PreS T cell epitope was inserted alone or with its C-terminal B cell epitope (132-145) at site 133 or 303 of MalE. The maltose-binding protein with PreS peptide inserts expressing the 120 to 132 sequence were able to induce in vivo and in vitro peptide-specific T cell response, whatever the length and the position of the insert. In the second model, the 103 to 115 T cell epitope from the C3 region of poliovirus type 1 (PV1) was inserted, with various flanking sequences, either at site 133 or 303 of MalE protein. The longer C3:86 to 115 insert induced poliovirus-specific T cell responses at both sites of MalE, whereas the C3:93 to 115 insert did it only at site 303 but not at site 133. Moreover, C3:103 to 115 specific T cell hybridomas discriminated between the processed peptides generated from the different chimeric proteins, as a result of differences in the length and the position of the inserted sequence. Therefore, in this experimental model the loss of in vivo immunogenicity of an antigenic determinant within a chimeric protein is related to the activation of a reduced T cell repertoire. These observations involve important consequences for the engineering of recombinant vaccines.
Influence of the angiotensin system on endothelial and smooth muscle cell migration. (1990)

The blood vessel wall's response to injury is an important determinant of luminal size and vessel function. The physiologic migration of endothelial cells from the edges of a wound and the pathophysiologic migration of medial smooth muscle cells into the intima are two important components of the vessel wall's response to injury. The influence of the angiotensin system on endothelial and smooth muscle cell migration have not been examined. In the present study, the influence of angiotensin system components on bovine aortic endothelial cell (BAEC) and bovine aortic smooth muscle cell (BASMC) migration after release of cultured cell monolayers from contact inhibition was determined. The angiotensin-converting enzyme (ACE) inhibitor lisinopril increased BAEC migration 41% +/- 3% (P less than 0.001), as did the specific angiotensin II antagonist sar1, ile8-angiotensin II (SAR) (41% +/- 3% (P less than 0.001). Exogenous angiotensin I and angiotensin II did not affect BAEC migration. Exogenous angiotensin II abolished the effect of lisinopril on BAEC migration. Lisinopril increased cell-associated u-plasminogen activator (u-PA) 23% +/- 3% (P less than 0.001) in migrating BAEC and angiotensin II abolished this increase. SAR increased u-PA 33% +/- 0% (P less than 0.001). In contrast, these agents had the opposite effect on smooth muscle cells. Angiotensin II increased smooth muscle cell migration 40% +/- 3% (P less than 0.001), and this effect was abolished by SAR. Angiotensin II also increased cell-associated u-PA 83% +/- 7% (P less than 0.001) in migrating BASMC. The increase in BAEC migration with inhibition of endothelial cell angiotensin II stimulation, either with lisinopril or SAR, also was associated with an increase in cell-associated u-PA. These results indicate that lisinopril interrupts an autocrine pathway in endothelial cells, in which endothelial cell-derived angiotensin I is converted to angiotensin II by ACE, and imply that angiotensin-converting enzyme inhibitors in vivo would act to reduce vessel wall injury by directly increasing the rate of endothelial cell wound closure; by increasing the antithrombotic tendency of the endothelium via enhanced u-PA; and indirectly, by decreasing production of angiotensin II and thereby the rate of smooth muscle cell migration into the intima.
Evaluation of beta-cell secretory capacity using glucagon-like peptide 1. (2000)

GLP-1 (2.5 nmol = 9 microg) elicits similar secretory responses to 1 mg glucagon (but has fewer side effects) and a standard meal. Additional elevation of plasma glucose to 15 mmol/l did not enhance the response further. The incremental response was similar to that elicited by arginine, but hyperglycemia had an additional effect on the response to arginine.
Development of a quantitative in vitro transformation assay for kidney epithelial cells (1992)

A quantitative in vitro transformation assay has been developed for the first time using primary rat kidney epithelial (RKE) cells. RKE cells were grown in a 50:50 mixture of 3T3 conditioned medium and DF8 medium composed of Ham's F-12/DMEM supplemented with ferrous sulfate, vasopressin, transferrin, sodium selenite and 10% fetal bovine serum. Colony forming efficiency of cells plated in this medium was high, ranging from 2.4 to 16%. Normal RKE cells treated with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) became transformed to a preneoplastic state of enhanced in vitro growth potential and formed large colonies of morphologically altered cells, whereas RKE cells treated with vehicle alone ceased proliferating and/or sloughed off the dish within 4-6 weeks. Relative survival and percent transformation frequency (Tf) of RKE cells exposed to MNNG were inversely proportional and both were dose dependent. MNNG concentration of 0.5, 1.0 and 2.0 micrograms/ml resulted in transformation frequencies of 0.13, 0.37 and 1.1% respectively (n = 4). Morphologically transformed colonies gave rise to cell lines with indefinite growth capacity and neoplastic potential. One of six transformed RKE cell (TRKE) lines injected into nude mice produced adenocarcinomas. This assay represents the first in vitro model for studying mechanisms of chemical transformation of normal kidney epithelial cells and may also be useful as a screen for identifying potential renal carcinogens.
A comparative, randomised, double-blind study of trazodone prolonged-release and paroxetine in the treatment of patients with major depressive disorder (2005)

This study showed that after a 6-week period trazodone and paroxetine are not different in reducing the symptoms of depression and, in many patients, in producing the remission of the illness. The known divergence in tolerability profile of the two medications, related to their differing pharmacological properties, was also confirmed. Trazodone may be of advantage in depressed patients with sleep difficulties.
Selective Water-Soluble Gelatinase Inhibitor Prodrugs (2011)

SB-3CT (1), a selective and potent thiirane-based gelatinase inhibitor, is effective in animal models of cancer metastasis and stroke; however, it is limited by poor aqueous solubility and extensive metabolism. We addressed these issues by blocking the primary site of metabolism and capitalizing on a prodrug strategy to achieve >5000-fold increased solubility. The amide prodrugs were quantitatively hydrolyzed in human blood to a potent gelatinase inhibitor, ND-322 (3). The arginyl amide prodrug (ND-478, 5d) was metabolically stable in mouse, rat, and human liver microsomes. Both 5d and 3 were nonmutagenic in the Ames II mutagenicity assay. The prodrug 5d showed moderate clearance of 0.0582 L/min/kg, remained mostly in the extracellular fluid compartment (Vd = 0.0978 L/kg), and had a terminal half-life of >4 h. The prodrug 5d had superior pharmacokinetic properties than those of 3, making the thiirane class of selective gelatinase inhibitors suitable for intravenous administration in the treatment of acute gelatinase-dependent diseases.
Homing by acoustic ranging to a single beacon (2002)

Homing and docking capabilities are essential in many autonomous underwater vehicle (AUV) applications. The paper tackles the homing problem, leaving aside the actual docking of the vehicle. Homing is often performed by means of acoustic sensors providing the bearing of the beacon to be reached in the vehicle frame. This measurement, combined with the vehicle's heading, is used directly to steer the AUV towards the goal. The algorithm described in the paper only uses acoustic range measurements to the beacon. The difficulties of this approach are due to the fact that a single range measurement does not completely constrain the beacon's position in the vehicle frame nor does it define the direction to follow. In addition, range measurements are noisy and sometimes spurious, and underwater currents affect dead-reckoning measurements. The AUV has then to maneuver, filter the range measurements and estimate the underwater current in order to maintain an estimation of the beacon's position. The homing procedure consists of obtaining an initial estimate of the beacon's position and of the underwater current components by appropriate maneuvers. The initial estimates are further refined during the actual displacement towards the beacon by means of a Kalman filter.
Color Management on the Desktop (1993)

As color input, display and output devices become more and more common the need for managing color becomes greater and greater. Color management refers to tools that support color matching, editing, preservation and storage. Color management offers the means of transmitting color images and documents containing color across local and wide area networks while maintaining the fidelity of the colors of the original image or document.The fundamental problem to be solved lies in the device dependent nature of color devices. That is, color is specified in RGB or CMYK without a standardized reference point to define the objective meaning of RGB or CMYK. This presentation will review the background problem of device dependence and the options to create device independent color images. Color management systems as application level solutions and as embedded aspects of operating sytems will be described. Apple's new ColorSync color extensions will be described as operating system level utilities to support color management.
Synthesis of 3′‐azido‐2′,3′‐dideoxy‐β‐D‐arabino‐hexopyranosyl nucleosides (1990)

Abstract The α,β‐unsaturated D ‐sugar aldehyde 2 , prepared from tri‐ O ‐acetyl‐ D ‐glucal, was converted into 1‐ O ‐acetyl‐3‐azido‐2,3‐dideoxy‐α‐ D ‐ arabino ‐pyranose ( 3 ) by reaction with sodium azide in a mixture of acetic acid and water followed by acetylation. Reaction of 3 with silylated pyrimidines using TMS triflate as catalyst followed by deprotection with saturated ammonia in methanol afforded 3′‐azido‐2′,3′‐dideoxy‐β‐ D ‐ arabino ‐hexopyranosyl nucleosides 4 .
Blood rheology in patients with transient ischemic attacks. (1988)

A complete ischemic stroke is associated with a significant hemorheologic disturbance leading to a rise of the viscous component of the peripheral resistance. This abnormality represents a consequence of the acute event. Nonetheless, it could be causally related to ischemia. In an attempt to clarify this question, 26 patients suffering from transient ischemic attacks were compared with controls in terms of blood and plasma viscosity, hematocrit, blood cell filterability, and erythrocyte aggregation. In patients there was a significant impairment of blood fluidity comprising plasma viscosity, blood cell filterability, and erythrocyte aggregation, suggesting that the flow properties of blood are jeopardized even before an acute stroke. Most likely this is due to the underlying arteriosclerotic process. Our results open the way to speculating that hemorheologic mechanisms might predispose to the development of a stroke by decreasing cerebral blood flow. If this hypothesis were true, it would have important therapeutic implications.
INDUCIBLE EXPRESSION OF AN ENDOTHELIAL CELL ANTIGEN ON MURINE MYOCARDIAL VASCULATURE IN ASSOCIATION WITH INTERSTITIAL CELLULAR INFILTRATION (1989)

LEPPINK, DOUGLAS M.; BISHOP, D. KEITH; SEDMAK, DANIEL D.; HENRY, MITCHELL L.; FERGUSON, RONALD M.; STREETER, PHILIP R.; BUTCHER, EUGENE C.; OROSZ, CHARLES G. Author Information
DNA vaccines: roles against diseases (2013)

Vaccination is the most successful application of immunological principles to human health. Vaccine efficacy needs to be reviewed from time to time and its safety is an overriding consideration. DNA vaccines offer simple yet effective means of inducing broad-based immunity. These vaccines work by allowing the expression of the microbial antigen inside host cells that take up the plasmid. These vaccines function by generating the desired antigen inside the cells, with the advantage that this may facilitate presentation through the major histocompatibility complex. This review article is based on a literature survey and it describes the working and designing strategies of DNA vaccines. Advantages and disadvantages for this type of vaccines have also been explained, together with applications of DNA vaccines. DNA vaccines against cancer, tuberculosis, Edwardsiella tarda, HIV, anthrax, influenza, malaria, dengue, typhoid and other diseases were explored.
A new DNA sequence assembly program (1995)

We describe the Genome Assembly Program (GAP), a new program for DNA sequence assembly. The program is suitable for large and small projects, a variety of strategies and can handle data from a range of sequencing instruments. It retains the useful components of our previous work, but includes many novel ideas and methods. Many of these methods have been made possible by the program's completely new, and highly interactive, graphical user interface. The program provides many visual clues to the current state of a sequencing project and allows users to interact in intuitive and graphical ways with their data. The program has tools to display and manipulate the various types of data that help to solve and check difficult assemblies, particularly those in repetitive genomes. We have introduced the following new displays: the Contig Selector, the Contig Comparator, the Template Display, the Restriction Enzyme Map and the Stop Codon Map. We have also made it possible to have any number of Contig Editors and Contig Joining Editors running simultaneously even on the same contig. The program also includes a new 'Directed Assembly' algorithm and routines for automatically detecting unfinished segments of sequence, to which it suggests experimental solutions.
Immunoglobulin domains inEscherichia coliand other enterobacteria: from pathogenesis to applications in antibody technologies (2012)

The immunoglobulin (Ig) protein domain is widespread in nature having a well-recognized role in proteins of the immune system. In this review, we describe the proteins containing Ig-like domains in Escherichia coli and enterobacteria, reporting their structural and functional properties, protein folding, and diverse biological roles. In addition, we cover the expression of heterologous Ig domains in E. coli owing to its biotechnological application for expression and selection of antibody fragments and full-length IgG molecules. Ig-like domains in E. coli and enterobacteria are frequently found in cell surface proteins and fimbrial organelles playing important functions during host cell adhesion and invasion of pathogenic strains, being structural components of pilus and nonpilus fimbrial systems and members of the intimin/invasin family of outer membrane (OM) adhesins. Ig-like domains are also found in periplasmic chaperones and OM usher proteins assembling fimbriae, in oxidoreductases and hydrolytic enzymes, ATP-binding cassette transporters, sugar-binding and metal-resistance proteins. The folding of most E. coli Ig-like domains is assisted by periplasmic chaperones, peptidyl-prolyl cis/trans isomerases and disulfide bond catalysts that also participate in the folding of antibodies expressed in this bacterium. The technologies for expression and selection of recombinant antibodies in E. coli are described along with their biotechnological potential.
Low residual noise speech enhancement utilizing time-frequency filtering (2002)

Spectral subtraction is a well known technique for enhancing speech corrupted by additive wideband noise. In this technique, the "clean" signal is approximated by subtracting a noise estimate from the spectrum of the corrupted signal. A negative side effect is the residual "musical" noise that is produced when isolated spectral peaks exceed the noise estimate. In this paper, a low residual noise enhancement method is presented. This method is based on spectral subtraction but incorporates an algorithm developed to suppress "musical" noise without affecting speech. The algorithm is referred to as time-frequency filtering because spectral peaks due to noise are eliminated on the basis of duration, bandwidth, and proximity to other peaks. Results showing the effects of combining spectral subtraction and time-frequency filtering are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Remote patient monitoring: Information reliability challenges (2009)

An increasing number of extramural applications in the personal healthcare domain pose new challenges regarding the security of medical data. In this paper, we focus on remote patient monitoring systems and the issues around information reliability. In these systems medical data is not collected by healthcare providers in a controlled medical environment using certified medical devices, but by patients at their homes without any supervision. Therefore, the healthcare professionals will need to place greater trust in information that patients report. To address this issue, we propose several approaches that minimize the risks and ensure high information reliability.
SLIC: an extensibility system for commodity operating systems (1998)

Modern commodity operating systems are large and complex systems developed over many years by large teams of programmers, containing hundreds of thousands of lines of code. Consequently, it is extremely difficult to add significant new functionality to these systems. In response to this problem, a number of recent research projects have explored novel operating system architectures to support untrusted extensions, including SPIN, VINO, Exokernel, and Fluke. Unfortunately, these architectures require substantialimplementation effort and are not generally available in commodity systems. In contrast, by leveraging the technique of interposition, we have designed and implemented a prototype extension system called SLIC which requires only trivial operating system
Evaluation of Abalone -Glucuronidase Substitution in Current Urine Hydrolysis Procedures (2014)

This study examined the potential of abalone β-glucuronidase as a viable and cost effective alternative to current hydrolysis procedures using acid, Helix pomatia β-glucuronidase and Escherichia coli β-glucuronidase. Abalone β-glucuronidase successfully hydrolyzed oxazepam-glucuronide and lorazepam-glucuronide within 5% of the spiked control concentration. Benzodiazepines present in authentic urine specimens were within 20% of the concentrations obtained with the current hydrolysis procedure using H. pomatia β-glucuronidase. JWH 018 N-(5-hydroxypentyl) β-d-glucuronide was hydrolyzed within 10% of the control concentration. Authentic urine specimens showed improved glucuronide cleavage using abalone β-glucuronidase with up to an 85% increase of drug concentration, compared with the results obtained using E. coli β-glucuronidase. The JWH 018 and JWH 073 carboxylic acid metabolites also showed increased drug concentrations of up to 24%. Abalone β-glucuronidase was able to completely hydrolyze a morphine-3-glucuronide control, but only 82% of total morphine was hydrolyzed in authentic urine specimens compared with acid hydrolysis results. Hydrolysis of codeine and hydromorphone varied between specimens, suggesting that abalone β-glucuronidase may not be as efficient in hydrolyzing the glucuronide linkages in opioid compounds compared with acid hydrolysis. Abalone β-glucuronidase demonstrates effectiveness as a low cost option for enzyme hydrolysis of benzodiazepines and synthetic cannabinoids.
Cooperative Assembly of Androgen Receptor into a Nucleoprotein Complex That Regulates the Prostate-specific Antigen Enhancer (1999)

Prostate cancer is characterized by elevated serum levels of prostate-specific antigen (PSA). PSA gene expression is controlled by an androgen-responsive transcriptional enhancer. Our study suggests that formation of a nucleoprotein complex, encompassing 170 base pairs of enhancer DNA, mediates androgen-responsive PSA enhancer activity. The complex is assembled by cooperative binding of androgen receptor to at least four tandem, nonconsensus androgen response elements (AREs). Systematic mutagenesis of the AREs demonstrated that they act synergistically to stimulate androgen receptor-responsive gene expression. We discuss a mechanism whereby a combination of high androgen receptor levels in the prostate and low affinity AREs contribute to the cell type specificity and activity of the enhancer.
The Chlamydomonas kinesin-like protein FLA10 is involved in motility associated with the flagellar membrane. (1995)

The Chlamydomonas FLA10 gene was shown to encode a flagellar kinesin-like protein (Walther, Z., M. Vashishtha, and J.L. Hall. 1994. J. Cell Biol. 126:175-188). By using a temperature-sensitive allele of FLA10, we have determined that the FLA10 protein is necessary for both the bidirectional movement of polystyrene beads on the flagellar membrane and intraflagellar transport (IFT), the bidirectional movement of granule-like particles beneath the flagellar membrane (Kozminski, K.G., K.A. Johnson, P. Forscher, and J.L. Rosenbaum. 1993. Proc. Natl. Acad. Sci. (USA). 90:5519-5523). In addition, we have correlated the presence and position of the IFT particles visualized by light microscopy with that of the electron dense complexes (rafts) observed beneath the flagellar membrane by electron microscopy. A role for FLA10 in submembranous or flagellar surface motility is also strongly supported by the immunolocalization of FLA10 to the region between the axonemal outer doublet microtubules and the flagellar membrane.
HOT JUPITER MAGNETOSPHERES (2011)

(Abridged) The upper atmospheres of close-in gas giant exoplanets are subjected to intense heating/tidal forces from their parent stars. Atomic/ionized hydrogen (H) layers are sufficiently rarefied that magnetic pressure may dominate gas pressure for expected planetary magnetic field strength. We examine the magnetospheric structure using a 3D isothermal magnetohydrodynamic model that includes: a static "dead zone" near the magnetic equator containing magnetically confined gas; a "wind zone" outside the magnetic equator in which thermal pressure gradients and the magneto-centrifugal-tidal effect give rise to transonic outflow; and a region near the poles where sufficiently strong tidal forces may suppress transonic outflow. Using dipole field geometry, we estimate the size of the dead zone to be ~1-10 planetary radii for a range of parameters. To understand appropriate base conditions for the 3D isothermal model, we compute a 1D thermal model in which photoelectric heating from the stellar Lyman continuum is balanced by collisionally-excited Lyman {\alpha} cooling. This 1D model exhibits a H layer with temperatures T=5000-10000K down to pressures of 10-100 nbar. Using the 3D isothermal model, we compute H column densities and Lyman {\alpha} transmission spectra for parameters appropriate to HD 209458b. Line-integrated transit depths of 5-10% can be achieved for the above base conditions. Strong magnetic fields increase the transit signal while decreasing the mass loss, due to higher covering fraction and density of the dead zone. In our model, most of the transit signal arises from magnetically confined gas, some of which may be outside the L1 equipotential. Hence the presence of gas outside the L1 equipotential does not directly imply mass loss. Lastly, we discuss the domain of applicability for the magnetic wind model described in this paper and in the Roche-lobe overflow model.