gebhart/patrepeval huggingface dataset:
Long-term culture and fine specificity of human cytotoxic T-lymphocyte clones reactive with human immunodeficiency virus type 1. (1989)

The definition of human immunodeficiency virus type 1 (HIV-1) immunogenic epitopes is central to the rational design of AIDS vaccine strategies. In this study, we have generated seven HIV-1 reverse transcriptase-specific cytotoxic T-lymphocyte (CTL) clones from the peripheral blood of two seropositive subjects. Epitopes recognized by these CTL clones were identified by using target cells infected with recombinant HIV-1-vaccinia virus vectors expressing truncated reverse transcriptase proteins and further defined by using target cells incubated with overlapping 25-amino acid synthetic reverse transcriptase peptides. Five different CTL epitopes were identified, and in each case recognition was restricted by class I human leukocyte antigens (HLA). Clones maintained specific cytolytic function in continuous culture for up to 11 months, requiring only periodic restimulation with a CD3-specific monoclonal antibody. These results indicate that HIV-1-specific, major histocompatibility class I-restricted CTL recognize multiple epitopes of a single viral gene product in conjunction with different host HLA antigens. In addition, they demonstrate that human virus-specific CTL can be grown in long-term culture without the need for reexposure to viral antigen.
Dihydroisoquinolinones: the design and synthesis of a new series of potent inhibitors of poly(ADP-ribose) polymerase. (1991)

A series of dihydroisoquinolinones, formally rigid analogs of 3-substituted benzamides, and a series of 2,3-disubstituted benzamides were synthesized and evaluated as inhibitors of poly(ADP-ribose) polymerase. The results indicated that the orientation of the amide with respect to the substituent on the aromatic ring was critical for optimum inhibitory activity. Selected compounds were also evaluated for their ability to modify the radiation response of mammalian cells to ionizing radiation. A number of the 5-substituted dihydroisoquinolinones, which were very potent inhibitors of the enzyme, were able to enhance the lethal effects of ionizing radiation in mammalian cells, as measured by changes in the survival curve parameters Do and/or Dq.
Pathway recognition and augmentation by computational analysis of microarray expression data (2005)

Data used in the paper may be downloaded from http://www.jainlab.org/downloads.html
Development and Test of Deployable Ultra-Lightweight CFRP-Booms for a Solar Sail (2000)

The Institute of Structural Mechanics of the Ger- man Aerospace Center is developing ultra lightweight, deploy- able boom structures made of carbon fibre-reinforced plastics (CFRP booms). Although the concept of CFRP booms can be universally applied to a number of tasks, its application in the development of a Solar Sail demonstrator and the results are pre- sented in this report. The CFRP booms have high bending and torsion stiffness and, additionally, the folding concept enables transportation within a very tight volume. Towards the end of 1999, it was possible to prove the use of the booms, by means of a 20x20 m 2 demonstrator, as an essential structurally mechani- cal part of a solar sail. The goal in the next phase of the project is the realisation of a 40x40 m 2 flyable version in 2004-2005.
Robot learning to walk: An architectural problem for intelligent controllers (2002)

The authors analyze the design premises of a new control architecture based on the principle of nested hierarchical control which has the feature of learning from the already programmed skills of a teleoperated system. Different architectural principles are explored and compared. It is shown how high level languages can be built from low level knowledge by using cooperation of the already existing skills, new expert knowledge (teaching new heuristics), and self-experience (example based) learning.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biodegradation and biocompatability of a calcium sulphate-hydroxyapatite bone substitute (2004)

An injectable material consisting of calcium sulphate mixed with hydroxyapatite was investigated as a possible alternative to autograft in the restoration of bone defects. The material was studied both in vitro in simulated body fluid (SBF) and in vivo when implanted in rat muscles and into the proximal tibiae of rabbits. Variation in the strength and weight of the material during ageing in SBF was measured. Tissue response, material resorption and bone ingrowth were studied in the animal models. A good tissue response was observed in both the rat muscles and rabbit tibiae without inflammatory reactions or the presence of fibrous tissue. Ageing in SBF showed that during the first week carbonated hydroxyapatite precipitated on the surfaces of the material and this may enhance bone ingrowth.
Friction and wear properties of polymer, metal, and ceramic prosthetic joint materials evaluated on a multichannel screening device (1981)

A 12-channel wear screening device was used to compare the wear properties of a variety of prosthetic joint materials. Two types of tests were run: (1) Ultrahigh molecular weight (UHMW) polyethylene bearing against metal or ceramic counterfaces and (2) various polymers bearing against 316 stainless steel as a standard counterface. Wear was quantified by weighing the polymer specimens, with presoaking and control-soak specimens used to minimize the error due to fluid absorption. The specimens were lubricated with bovine blood serum. Friction and polyethylene wear was very low with each of the metals (316 stainless steel, cobalt-chrome alloy, multiphase alloy, and titanium 6-4 alloy) such that the differences in wear rate would not be significant in terms of choosing a material for clinical application. However, titanium 6-4 alloy was found to be especially susceptible to abrasive wear by particles of acrylic cement. Nitrided titanium 6-4 counterfaces were impervious to acrylic abrasion. Polyethylene wear against highly polished, fully dense ceramics (Sialon, Alumina, Macor, and pyrolytic graphite) was as low as that with the metal counterfaces. Wear increased slightly with increasing ceramic surface roughness. The coefficient of friction of polyethylene against pyrolytic graphite was two to three times higher than with the metals or other ceramics. All of the alternate polymers underwent more wear than UHMW polyethylene. Teflon and polyester, two polymers that have proven unsuccessful in prior clinical use, had wear rates 1,600 and 830 times greater than polyethylene, respectively, an indication that the laboratory wear test provided a quantitative prediction of the behavior of the materials in vivo. However, it was difficult to assess the clinical significance of the less extreme wear rates since the ability of the tissues encapsulating a prosthesis to accomodate wear debris is not known on a quantitative basis.
Integrating security in CORBA based object architectures (2002)

We propose a distributed security architecture for incorporation into object oriented distributed computing systems, and in particular, into OMG's CORBA based object architectures. The primary objective of the security architecture is to make CORBA resilient to both component failures and malicious attacks. The core of the architecture is the notion of secure ORB node-an ORB node enhanced with "pluggable" system security objects interacting through generic security service APIs. System security objects coupled with protocols among them facilitate creation and management of clients, objects, and security information. Security services addressed in the paper include, but are in no way limited to, client/object authentication, access control, and integrity and confidentiality protections.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Relationship Between Allan Variances and Kalman Filter Parameters (1984)

A relationship was constructed between the Allan variance parameters (H sub z, H sub 1, H sub 0, H sub -1 and H sub -2) and a Kalman Filter model that would be used to estimate and predict clock phase, frequency and frequency drift. To start with the meaning of those Allan Variance parameters and how they are arrived at for a given frequency source is reviewed. Although a subset of these parameters is arrived at by measuring phase as a function of time rather than as a spectral density, they all represent phase noise spectral density coefficients, though not necessarily that of a rational spectral density. The phase noise spectral density is then transformed into a time domain covariance model which can then be used to derive the Kalman Filter model parameters. Simulation results of that covariance model are presented and compared to clock uncertainties predicted by Allan variance parameters. A two state Kalman Filter model is then derived and the significance of each state is explained.
ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites (2011)

ZFN-Site facilitates genome searches for possible ZFN cleavage sites based on user-defined stringency limits. ZFN-Site is an improvement over other methods because the FetchGWI search engine uses an indexed search of genome sequences for all ZFN target sites and possible off-target sites matching the half-sites and stringency limits. Therefore, ZFN-Site does not miss potential off-target sites.
Data structures for physical representation of VLSI (1990)

This paper surveys data structures currently being used to represent the physical design of integrated circuits. They are evaluated in terms of storage requirements and processing costs. For developing a new generation of layout tools, these data structures must be reconsidered, in orfer to cope with the advances in new technologies such as gallium arsenide and integrated optics. Therefore, the potentialities of these data stuctures in handling new layout requirements are investigated; for example in representing computer-generated holograms for optical conncection of VLSI
Activation of Caspases in Lethal Experimental Hepatitis and Prevention by Acute Phase Proteins (1999)

Lethal hepatitis can be induced by an agonistic anti-Fas Ab in normal mice or by TNF in mice sensitized to d -(+)-galactosamine or actinomycin D. In all three models, we found that apoptosis of hepatocytes is an early and necessary step to cause lethality. In the three models, we observed activation of the major executioner caspases-3 and -7. Two acute-phase proteins, alpha1-acid glycoprotein and alpha1-antitrypsin, differentially prevent lethality: alpha1-acid glycoprotein protects in both TNF models and not in the anti-Fas model, while alpha1-antitrypsin confers protection in the TNF/d -(+)-galactosamine model only. The protection is inversely correlated with activation of caspase-3 and caspase-7. The data suggest that activation of caspase-3 and -7 is essential in the in vivo induction of apoptosis leading to lethal hepatitis and that acute phase proteins are powerful inhibitors of apoptosis and caspase activation. Furthermore, Bcl-2 transgenic mice, expressing Bcl-2 specifically in hepatocytes, are protected against a lethal challenge with anti-Fas or with TNF/d -(+)-galactosamine, but not against TNF/actinomycin D. The acute-phase proteins might constitute an inducible anti-apoptotic protective system, which in pathology or disturbed homeostasis prevents excessive apoptosis.
Buildup of Ultrathin Multilayer Films by a Self‐Assembly Process: II. Consecutive Adsorption of Anionic and Cationic Bipolar Amphiphiles and Polyelectrolytes on Charged Surfaces (1991)

Abstract We have recently reported on the consecutive physisorption of anionic and cationic bipolar amphiphiles onto charged surfaces, adsorbed out of aqueous solutions [1]. Here, we extend our previous concept to multipolar compounds such as polyelectrolytes. In contrast to the bipolar amphiphile system, it is not necessary to separate single charges by a rigid unit, when the polyelectrolyte is adsorbed from sufficiently concentrated solutions. In this case the physisorbed layer does not bind with all ionic groups to the surface and exposes free ionic groups at the new film/solution interface. Therefore a polyelectrolyte layer can replace a layer of bipolar amphiphiles in the consecutive buildup of a multilayered assembly. The buildup of multilayers can then be described as follows: A solid substrate with a positively charged planar surface is immersed in the solution containing the negatively charged bipolar amphiphile, a monolayer of the amphiphile is adsorbed and due to its bipolar structure the surface charge is reversed. After rinsing in pure water the substrate is immersed in the solution containing the positively charged polyelectrolyte. Again a monolayer is adsorbed but now the original surface charge is restored. By repeating both steps in a cyclic fashion alternating multilayer assemblies of both compounds are obtained. In the same way multilayer assemblies can be prepared by using negatively charged polyelectrolytes and positively charged bipolar amphiphiles. It is demonstrated that multilayer films composed of at least 39 consecutively alternating layers, which corresponds to a total film thickness of 151 nm, can be assembled.
TGF-β1 induces lens cells to accumulate α-smooth muscle actin, a marker for subcapsular cataracts (1994)

Spindle-shaped myofibroblast-like cells, which contain alpha-smooth muscle actin, have been described in anterior subcapsular cataract and after-cataract. In a previous study in this laboratory, it was shown that transforming growth factor-beta (TGF beta) induces the formation of spindle-shaped cells in lens epithelial explants. The aim of this investigation was to determine whether these TGF beta-induced spindle-shaped cells contain alpha-smooth muscle actin. Lens epithelial explants were prepared from 21-day-old rats and cultured with either TGF beta 1 or basic FGF alone, a combination of both growth factors, or without added growth factors. After three days, cellular changes were monitored by phase contrast microscopy, localisation of filamentous actin with rhodamine-phalloidin, and immunolocalisation and immunoblotting of alpha-smooth muscle actin. TGF beta induced rapid cell elongation and formation of characteristic spindle-shaped cells in lens epithelial explants in the presence or absence of FGF. These cells contained alpha-smooth muscle actin, a marker for myofibroblastic cells and a protein not normally found in the lens. The present study thus provides molecular evidence that TGF beta induces cataractous changes in lens epithelial cells. As TGF beta is potentially available to lens cells in situ throughout life, these findings are consistent with a key role for TGF beta in the aetiology of major forms of subcapsular cataract.
Molecular cloning and expression of palmitoyl-protein thioesterase. (1994)

We have previously reported the purification of a palmitoyl-protein thioesterase (PPT) from bovine brain that removes palmitate from Ha-Ras (Camp, L. A., and Hofmann, S. L. (1993) J. Biol. Chem. 268, 22566-22574). In the current paper, we have isolated bovine and rat cDNA clones encoding PPT. The deduced amino acid sequence of PPT predicts a protein of 306 amino acids that contains amino acid motifs characteristic of thioesterases: "Gly-X-Ser-X-Gly" positioned near the NH2 terminus and "Gly-Asp-His" positioned near the COOH terminus of the protein. The identity of the PPT cDNA was further confirmed by expression in simian COS cells and insect Sf9 cells. Comparison of the DNA and protein sequence data suggests that a hydrophobic NH2-terminal sequence of 27 amino acid residues is removed from the primary translation product. Furthermore, the recombinant protein and the native protein purified from bovine brain contain complex asparagine-linked oligosaccharides and a large proportion of the expressed PPT is secreted from COS and Sf9 cells. Thus, while the palmitoyl-protein thioesterase will deacylate intracellular palmitoylated proteins such as Ha-Ras and the alpha subunits of heterotrimeric G proteins, the physiologic substrates are likely to be externally oriented or secreted proteins.
Progress in understanding structure–function relationships in respiratory chain complex II (2000)

Complex II (succinate:quinone oxidoreductase) of aerobic respiratory chains oxidizes succinate to fumarate and passes the electrons directly into the quinone pool. It serves as the only direct link between activity in the citric acid cycle and electron transport in the membrane. Finer details of these reactions and interactions are but poorly understood. However, complex II has extremely similar structural and catalytic properties to quinol:fumarate oxidoreductases of anaerobic organisms, for which X-ray structures have recently become available. These offer new insights into structure-function relationships of this class of flavoenzymes, including evidence favoring protein movement during catalysis.
Multi-beam switched parasitic antenna embeddedindielectric for wireless communications systems (2001)

A nine monopole antenna embedded in a dielectric cylinder mounted on a small ground plane has been designed for IEEE 802.11 applications. Two simultaneous beams are controlled electronically with a front-to-back ratio of 12 dB and 13% bandwidth. The dielectric reduced the footprint by 85% and the antenna volume by 91% compared to an array with similar functionality in air.
Generation of functional NKT cells in vitro from embryonic stem cells bearing rearranged invariant Vα14-Jα18 TCRα gene (2009)

Establishment of a system with efficient generation of natural killer T (NKT) cells from embryonic stem (ES) cells would enable us to identify the cells with NKT-cell potential and obtain NKT cells with desired function. Here, using cloned ES (NKT-ES) cells generated by the transfer of nuclei from mature NKT cells, we have established a culture system that preferentially developed functional NKT cells and also identified early NKT progenitors, which first appeared on day 11 as a c-kit(+) population in the cocultures on OP9 cells with expression of Notch ligand, delta-like1 (OP9/Dll-1) and became c-kit(lo/-) on day 14. Interestingly, in the presence of Notch signals, NKT-ES cells differentiated only to thymic CD44(lo) CD24(hi) NKT cells producing mainly interleukin-4 (IL-4), whereas NKT cells resembling CD44(hi) CD24(lo) liver NKT cells producing mainly interferon gamma (IFN-gamma) and exhibiting strong adjuvant activity in vivo were developed in the switch culture starting at day 14 in the absence of Notch. The cloned ES culture system offers a new opportunity for the elucidation of the molecular events on NKT-cell development and for the establishment of NKT-cell therapy.
von Willebrand Factor–Cleaving Protease in Thrombotic Thrombocytopenic Purpura and the Hemolytic–Uremic Syndrome (1998)

Nonfamilial thrombotic thrombocytopenic purpura is due to an inhibitor of von Willebrand factor-cleaving protease, whereas the familial form seems to be caused by a constitutional deficiency of the protease. Patients with the hemolyticuremic syndrome do not have a deficiency of von Willebrand factor-cleaving protease or a defect in von Willebrand factor that leads to its resistance to protease.
Diminution of mouse epidermal superoxide dismutase and catalase activities by tumor promoters (1981)

The effects of phorbol ester tumor promoters and related compounds on superoxide dismutase (SOD) and catalase were examined. The treatment of adult mouse skin with 2 micrograms 12-O-tetradecanoylphorbol-13-acetate (TPA) resulted in a sustained decrease in the basal levels of both SOD and catalase activities in the epidermis. A decline in SOD activity occurred within 3 h after application and the maximum effect was seen at 16--17 h. The decrease in SOD activity was always accompanied by a similar decline in the epidermal catalase activity. The alterations in both enzymes occurred against a high background of enhanced protein synthesis which indicates that the effect of TPA is selective for SOD and catalase. Other tumor promoters such as phorbol 12,13-dibutyrate and the non-phorbol tumor promoter anthraline also lowered the activities of both the enzymes. Mezerein, a resiniferonol derivative with weak promoting activity but a potent stage-II promoter, appeared to be more potent than TPA in lowering the basal levels. These results indicate that damage which favors neoplastic progression could occur in TPA-treated mouse skin due to the accumulation of free radicals resulting from low levels of SOD and catalase activity. In addition, the TPA-caused decrease in the levels of SOD and catalase was not prevented by either retinoic acid, fluocinolone acetonide, tosyl amino-2-phenylethyl chloromethyl ketone, or butylated hydroxytoluene, suggesting that inhibition of tumor promotion by these agents is not mediated through alterations in the levels of enzymatic activities which decrease free radical concentrations.
Concentrations of Serum Granulocyte-Colony-Stimulating Factor in Normal Pregnancy and Preeclampsia (1999)

Serum concentrations of G-CSF are increased in normal and, even more so, in preeclamptic pregnancies. Because there was no relationship between serum G-CSF concentration and the number of leukocytes, G-CSF might act not to promote the physiological leukocytosis of pregnancy, but to stimulate the function of leukocytes such as phagocytosis. Moreover, it might be that G-CSF plays important roles in the activation of granulocytes or vascular endothelial injury, which are considered to be important pathological conditions in the development of preeclampsia.
Emission physics of the thermionic energy converter (1963)

Emission processes establish the upper limit of the performance obtainable in the thermionic converter. This paper briefly introduces the basic factors which must be considered to achieve this limit and outlines recent developments in the related technology. The basic elements of thermal excitation common to these processes are outlined and the results are used to illustrate the interdependence of the atom, electron and ion emission processes. The constraints imposed by this interdependence imply the existence of a natural limitation on vaporization lifetime for efficient operation using elementary emitter materials. This limitation is overcome by the use of emitters with an adsorbed layer of cesium and constraints imposed by the interdependence of the emission processes prescribe regions of efficient operation of these emitters. Consideration of the basic processes occurring in the adsorbed layer permits semiquantitative evaluation of the relative merit of different materials for use as emitters and collectors. The effect of nonuniform surfaces is reviewed and work in progress to understand the nature and origin of the nonuniformities is discussed. Substantial improvement in converter performance and reproducibility is possible through the development of uniform and optimum electrode surfaces.