gebhart/patrepeval huggingface dataset:
Multiple rearrangements in T cell receptor alpha chain genes maximize the production of useful thymocytes. (1993)

Peripheral T lymphocytes each express surface T cell receptor (TCR) alpha and beta chains of a single specificity. These are produced after random somatic rearrangements in TCR alpha and beta germline genes. Published model systems using mice expressing TCR alpha and/or beta chain transgenes have shown that allelic exclusion occurs conventionally for TCR-beta. TCR alpha chain expression, however, appears to be less strictly regulated, as endogenous TCR alpha chains are often found in association with transgenic TCR beta chains in TCR alpha/beta transgenic mice. This finding, coupled with the unique structure of the TCR alpha locus, has led to the suggestion that unlike TCR beta and immunoglobulin heavy chain genes, TCR alpha genes may make multiple rearrangements on each chromosome. In the current study, we demonstrate that the majority of TCR-, noncycling thymocytes spontaneously acquire surface expression of CD3/TCR. Further, we show that cultured immature thymocytes originally expressing specific TCR alpha and beta chains may lose surface expression of the original TCR alpha, but not beta chains. These data provide evidence that not only must multiple rearrangements occur, but that TCR alpha gene rearrangement continues even after surface expression of a TCR alpha/beta heterodimer, apparently until the recombination process is halted by positive selection, or the cell dies. Sequential rearrangement of TCR alpha chain genes facilitates enhanced production of useful thymocytes, by increasing the frequency of production of both in-frame rearrangements and positively selectable TCR alpha/beta heterodimers.
A 130-MHz 8-b CMOS video DAC for HDTV applications (1991)

In order to achieve monotonicity and a high-speed performance, a current-cell matrix configuration and a parallel decoding circuit with one-stage latches have been used. A deglitching circuit has been introduced in the decoding stages to guarantee a low glitch energy. P-channel devices used as current sources ensure a low noise level and a ground-referenced voltage output in a doubly terminated 75- Omega transmission line. Experimental results have shown that the maximum conversion rate is 130 MHz and the integral and differential linearity errors are less than 0.5 LSB. The maximum glitch energy is 50 pS-V. The DAC has been developed in a 1- mu m digital/analog CMOS technology. The entire circuit dissipates 150 mW at a 130-MHz conversion rate while operating from a single 5-V power supply.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Critical evaluation of the pulsed laser method for single event effects testing and fundamental studies (1994)

In this paper we present an evaluation of the pulsed laser as a technique for single events effects (SEE) testing. We explore in detail the important optical effects, such as laser beam propagation, surface reflection, and linear and nonlinear absorption, which determine the nature of laser-generated charge tracks in semiconductor materials. While there are differences in the structure of laser- and ion-generated charge tracks, we show that in many cases the pulsed laser remains an invaluable tool for SEE testing. Indeed, for several SEE applications, we show that the pulsed laser method represents a more practical approach than conventional accelerator-based methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibition of Monometalated Methionine Aminopeptidase:  Inhibitor Discovery and Crystallographic Analysis (2007)

Two divalent metal ions are commonly seen in the active-site cavity of methionine aminopeptidase, and at least one of the metal ions is directly involved in catalysis. Although ample structural and functional information is available for dimetalated enzyme, methionine aminopeptidase likely functions as a monometalated enzyme under physiological conditions. Information on structure, as well as catalysis and inhibition, of the monometalated enzyme is lacking. By improving conditions of high-throughput screening, we identified a unique inhibitor with specificity toward the monometalated enzyme. Kinetic characterization indicates a mutual exclusivity in binding between the inhibitor and the second metal ion at the active site. This is confirmed by X-ray structure, and this inhibitor coordinates with the first metal ion and occupies the space normally occupied by the second metal ion. Kinetic and structural analyses of the inhibition by this and other inhibitors provide insight in designing effective inhibitors of methionine aminopeptidase.
A New Negative-Type Photosensitive Polyimide Based on Poly(hydroxyimide), a Cross-Linker, and a Photoacid Generator (1996)

A negative working photosensitive polyimide based on poly(hydroxyimide) (PHI), 2,6-bis(hydroxymethyl)-4-methylphenol (BHMP) as cross-linker, and photoacid generator diphenyliodonium 9,10-dimethoxyanthracene-2-sulfonate (DIAS) has been developed. The PHI was prepared by the ring-opening polyaddition of 4,4‘-hexafluoroisopropylidenebis(phthalic anhydride) and 4,4‘-diamino-4‘‘-hydroxytriphenylmethane, followed by thermal cyclization in refluxing xylene. The PHI film showed excellent transparency to UV light. The photosensitive polyimide containing 70 wt % PHI, 20 wt % BHMP, and 10 wt % DIAS showed a sensitivity of 70 mJ/cm2 and a contrast of 3.8 when it was exposed to 365 nm light and postbaked at 120 °C, followed by developing with a 2.5% aqueous tetramethylammonium hydroxide solution at 40 °C. The mechanistic study on the formation of images is also discussed.
Defect dominated charge transport in amorphous Ta2O5 thin films (2000)

Ta 2 O 5 is a candidate for use in metal–oxide–metal (MOM) capacitors in several areas of silicon device technology. Understanding and controlling leakage current is critical for successful implementation of this material. We have studied thermal and photoconductive charge transport processes in Ta2O5 MOM capacitors fabricated by anodization, reactive sputtering, and chemical vapor deposition. We find that the results from each of these three methods are similar if one compares films that have the same thickness and electrodes. Two types of leakage current are identified: (a) a transient current that charges the bulk states of the films and (b) a steady state activated process involving electron transport via a defect band. The transient process involves either tunneling conductivity into states near the Fermi energy or ion motion. The steady state process, seen most commonly in films &amp;lt;300 Å thick, is dominated by a large number of defects, ∼1019–1020 cm−3, located near the metal–oxide interfaces. The interior of thick Ta2O5 films has a substantially reduced number of defects. Modest heating (300–400 °C) of Ta2O5 in contact with a reactive metal electrode such as Al, Ti, or Ta results in interfacial reactions and the diffusion of defects across the thickness of the film. These experiments show that successful integration of Ta2O5 into semiconductor processing requires a better understanding of the impact of defects on the electrical characteristics and a better control of the metal–Ta2O5 interface.
Optimal Rate Adaptation for Hybrid ARQ in Time-Correlated Rayleigh Fading Channels (2011)

Most analytical studies on hybrid automatic repeat request (HARQ) have been carried out in either slow fading or fast fading assumptions. However, since practical wireless channels typically exhibit a time-correlated property, we need to take into account the effects of time correlation in the design of HARQ. In this paper, we analyze the outage probability and delay-limited throughput of HARQ with rate adaptation in a time-correlated channel model. Then, we propose a rate adaptation scheme to maximize the delay-limited throughput and evaluate the performance of the proposed scheme under a delay constraint. Our analytical and numerical results show that the proposed rate adaptation scheme outperforms the conventional rate adaptation schemes. The proposed rate adaptation scheme is further simplified by using a Gaussian approximation on the effective channel power gain. The rate adaptation based on the proposed Gaussian approximation reduces the complexity and achieves a throughput gain comparable to that with the exact channel distributions.
Molecular mechanisms of apolipoprotein B mRNA editing (2001)

A site-specific post-transcriptional cytidine to uridine deamination reaction is responsible for the production of apolipoprotein B48 in the mammalian small intestine. The molecular machinery responsible for apolipoprotein B RNA editing consists of apobec-1, an RNA-specific cytidine deaminase that functions in conjunction with a recently identified protein referred to as ACF/ASP. These proteins together represent the minimal editing enzyme, although other proteins may associate with the enzyme complex. Apobec-1 is a member of a supergene family of cytidine deaminases, with several homologs recently identified in the human genome. ACF/ASP is novel, and emerging information reveals interesting clues to its role in the apolipoprotein B RNA editing enzyme complex.
Increased Expression of DNA Cointroduced with Nuclear Protein in Adult Rat Liver (1989)

DNA and nuclear proteins were transferred into cells simultaneously at more than 95% efficiency by means of vesicle complexes. The DNA was rapidly transported into the nuclei of cultured cells, and its expression reached a maximum within 6 to 8 hours after its introduction. Moreover, when the plasmid DNA and nuclear protein were cointroduced into nondividing cells in rat liver by injection into the portal veins of adult rats, the plasmid DNA was carried into liver cell nuclei efficiently by nuclear protein. The expression of the DNA in adult rat liver, on introduction of the DNA with nuclear protein, was more than five times as great as with nonnuclear protein.
Deterministic Ratchet for Sub-micrometer (Bio)particle Separation (2018)

Resolving the heterogeneity of particle populations by size is important when the particle size is a signature of abnormal biological properties leading to disease. Accessing size heterogeneity in the sub-micrometer regime is particularly important to resolve populations of subcellular species or diagnostically relevant bioparticles. Here, we demonstrate a ratchet migration mechanism capable of separating sub-micrometer sized species by size and apply it to biological particles. The phenomenon is based on a deterministic ratchet effect, is realized in a microfluidic device, and exhibits fast migration allowing separation in tens of seconds. We characterize this phenomenon extensively with the aid of a numerical model allowing one to predict the speed and resolution of this method. We further demonstrate the deterministic ratchet migration with two sub-micrometer sized beads as model system experimentally as well as size-heterogeneous mouse liver mitochondria and liposomes as model system for other organelles. We demonstrate excellent agreement between experimentally observed migration and the numerical model.
Preparation and Testing of Monoclonal Antibodies to Recombinant Proteins (1998)

Monoclonal antibodies (MAbs) are essential reagents for the isolation, identification, and cellular localization of specific gene products and for aiding in the determination of their macromolecular structure. They can also help in identifying the function of the protein. Although the ability to clone and sequence specific genes has revolutionized our understanding of cellular structure and function, the preparation of recombinant proteins and the synthesis of peptides based on protein sequences derived from cDNA clones have provided sufficient material for generating specific antibodies. The proteins may be isolated and purified directly from cells, or recombinant proteins may be derived from prokaryotic systems, such as Escherichia coli, or from eukaryotic expression systems, such as Chinese hamster ovary (CHO) cells, or insect cells expressing constructs in baculovirus. The eukaryotic systems are being used increasingly for expression of glycoproteins, because the recombinant material is glycosylated. It should be remembered, however, that glycosylation may be species-specific and if one of the functions of the protein depends on carbohydrate, then the function of a recombinant glycoprotein may be altered depending on the species used for expression.
Processing of the Ebola virus glycoprotein by the proprotein convertase furin (1998)

In the present study, we have investigated processing and maturation of the envelope glycoprotein (GP) of Ebola virus. When GP expressed from vaccinia virus vectors was analyzed by pulse-chase experiments, the mature form and two different precursors were identified. First, the endoplasmic reticulum form preGPer, full-length GP with oligomannosidic N-glycans, was detected. preGPer (110 kDa) was replaced by the Golgi-specific form preGP (160 kDa), full-length GP containing mature carbohydrates. preGP was finally converted by proteolysis into mature GP1,2, which consisted of two disulfide-linked cleavage products, the amino-terminal 140-kDa fragment GP1, and the carboxyl-terminal 26-kDa fragment GP2. GP1,2 was also identified in Ebola virions. Studies employing site-directed mutagenesis revealed that GP was cleaved at a multibasic amino acid motif located at positions 497 to 501 of the ORF. Cleavage was blocked by a peptidyl chloromethylketone containing such a motif. GP is cleaved by the proprotein convertase furin. This was indicated by the observation that cleavage did not occur when GP was expressed in furin-defective LoVo cells but that it was restored in these cells by vector-expressed furin. The Reston subtype, which differs from all other Ebola viruses by its low human pathogenicity, has a reduced cleavability due to a mutation at the cleavage site. As a result of these observations, it should now be considered that proteolytic processing of GP may be an important determinant for the pathogenicity of Ebola virus.
Modulation of differentiation by exogenous agents (1990)

VOLUME II: MODULATION of DIFFERENTIATION by EXOGENOUS AGENTS Modulation of Differentiation: Potential Mechanism by Which Inferferons Induce Antitumor Activity Regulation of Tumor Antigen Expression by Recombinant Interferons Induction of Terminal Differentiation of Human Leukemic Cells by Chemotherapeutic and Cytotoxic Drugs Induced Differentiation of Transformed Cells with Polar/Apolar Compounds and the Reversibility of the Transformed Phenotype 5-Azacytidine Induction of Differentiation in Fibroblast Cells by Irradiation and Chemical Carcinogens The Early Reactions and Factors Involved in In Vitro Erythroid Differentiation of Mouse Erythroleukemia (MEL) Cells Regulation of Cell Contacts, Cell Configuration and Cytoskeletal Gene Expression in Differentiating Systems Macrophage and Granulocyte Macrophage-Colony Stimulating Factor Effects on Human Monocyte Differentiation Regulation of Phenotype by Transforming Growth Factor-b: Role of the Extracellular Matrix
Palladium-Catalyzed Cross-Coupling of Benzylzinc Reagents with Methylthio N-Heterocycles: A New Coupling Reaction with Unusual Selectivity (2000)

Benzylzinc reagents undergo palladium-catalyzed cross-coupling reactions with methylthio-substituted N-heterocycles in moderate to good yields. 2-(Methylthio)pyrimidines are particularly reactive substrates for this reaction. As a result, the regioselectivity of 2,4-bis(methylthio)pyrimidines is opposite to that of their 2,4-dichloropyrimidine analogues. This unusual cross-coupling reaction offers new flexibility in the regioselective synthesis of substituted pyrimidines and other heterocycles.
Measuring wavelet phase from seismic data (1988)

Geophysicists are well into their second decade of serious interest in the seismic wavelet. Several requirements — to invert seismic complexes into their causative reflection series, to do stratigraphic modeling, to correct section displays to zero phase form, to standardize data of different vintages for composite structural mapping — put a knowledge of the basic wavelet shape, which can provide the way to satisfy these needs, near the top of every wish list. Ever since the convolutional model, with its basic wavelet and reflectivity series concepts, was proposed more than 30 years ago, there has been some kind of continuous effort to estimate the wavelet in a reliable and convenient manner. In spite of this constant attention, wavelets today are usually determined by directly measuring them in the field, or by estimating them in the processing environment through assuming their phase properties. Phase assumptions always leave the serious wavelet estimator a little queasy. He is always looking for some data that is independent of the seismic records to test these phase assumptions and, hopefully, certify one as being adequate for the job at hand.
Scientific basis for the therapeutic use of Withania somnifera (ashwagandha): a review. (2000)

Preliminary studies have found various constituents of ashwagandha exhibit a variety of therapeutic effects with little or no associated toxicity. These results are very encouraging and indicate this herb should be studied more extensively to confirm these results and reveal other potential therapeutic effects. Clinical trials using ashwagandha for a variety of conditions should also be conducted.
Small Particulate Gadolinium Oxide and Gadolinium Oxide Albumin Microspheres as Multimodal Contrast and Therapeutic Agents (2003)

Use of SPGO and SPGO encapsulated in non-heat-hardened albumin microspheres (GOAM) represents a new approach. SPGO and GOAM have suitable physicochemical properties to warrant further biophysical and animal studies and reevaluation of toxicity limitations.
The D-Galactosamine Loaded Mouse and Its Enhanced Sensitivity to Lipopolysaccharide and Monophosphoryl Lipid A: A Role for Superoxide (1991)

Mice are relatively resistant to the lethal effects of endotoxin. Sensitivity to lipopolysaccharide (LPS) and monophosphoryl lipid A (MPL) can be enhanced by concurrently loading animals with D-galactosamine (D-gal). Significant diurnal variation in susceptibility to lethal toxicity was observed in D-gal loaded mice upon LPS or MPL immunostimulant challenge. In mice treated with either MPL or MPL plus D-gal, at the time of greatest toxic sensitivity, serum TNF levels were significantly higher than was seen in mice treated at a time of low sensitivity. Peritoneal exudate cells (PECs) harvested from mice treated with either D-gal or MPL displayed enhanced in vitro superoxide (SO) production. Simultaneous treatment with D-gal and MPL led to a synergistic enhancement of SO production above that induced by either xenobiotic alone. Pretreatment with the SO dismutase mimetic Cu(II) (diisopropyl salicylate)2 significantly protected mice from the lethal toxicity of D-gal-MPL challenge. PECs harvested from these same mice failed to display the elevated in vitro SO production reported above. SO elaboration in vivo, presumably by hepatocytes, PECs, and possibly other cells, subsequent to D-gal loading and LPS or MPL challenge, appears to play an important role in the lethal toxicity observed. The diurnal variation in toxicity reported in this animal model may result from TNF modulation of SO production in vivo.
Ethanol Plus Caffeine (Caffeinol) for Treatment of Ischemic Stroke (2003)

Low doses of caffeinol, equivalent to no more than 2 to 3 cups of strong coffee and 1 cocktail, are consistently and highly neuroprotective, are well tolerated, can be added to other therapies to increase the effect of each, and do not interfere with or complicate rtPA therapy. Caffeinol is an appropriate candidate for clinical trial in stroke patients, although it may be less effective in patients with regular alcohol intake.
Recruitment of Gr-1+ monocytes is essential for control of acute toxoplasmosis (2005)

Circulating murine monocytes comprise two largely exclusive subpopulations that are responsible for seeding normal tissues (Gr-1-/CCR2-/CX3CR1high) or responding to sites of inflammation (Gr-1+/CCR2+/CX3CR1lo). Gr-1+ monocytes are recruited to the site of infection during the early stages of immune response to the intracellular pathogen Toxoplasma gondii. A murine model of toxoplasmosis was thus used to examine the importance of Gr-1+ monocytes in the control of disseminated parasitic infection in vivo. The recruitment of Gr-1+ monocytes was intimately associated with the ability to suppress early parasite replication at the site of inoculation. Infection of CCR2-/- and MCP-1-/- mice with typically nonlethal, low doses of T. gondii resulted in the abrogated recruitment of Gr-1+ monocytes. The failure to recruit Gr-1+ monocytes resulted in greatly enhanced mortality despite the induction of normal Th1 cell responses leading to high levels of IL-12, TNF-alpha, and IFN-gamma. The profound susceptibility of CCR2-/- mice establishes Gr-1+ monocytes as necessary effector cells in the resistance to acute toxoplasmosis and suggests that the CCR2-dependent recruitment of Gr-1+ monocytes may be an important general mechanism for resistance to intracellular pathogens.
Seaweed resistance to microbial attack: A targeted chemical defense against marine fungi (2003)

Pathogenic microbes can devastate populations of marine plants and animals. Yet, many sessile organisms such as seaweeds and sponges suffer remarkably low levels of microbial infection, despite lacking cell-based immune systems. Antimicrobial defenses of marine organisms are largely uncharacterized, although from a small number of studies it appears that chemical defenses may improve host resistance. In this study, we asked whether the common seaweed Lobophora variegata is chemically defended against potentially deleterious microorganisms. Using bioassay-guided fractionation, we isolated and characterized a 22-membered cyclic lactone, lobophorolide (1), of presumed polyketide origin, with sub-microM activity against pathogenic and saprophytic marine fungi. Deterrent concentrations of 1 were found in 46 of 51 samples collected from 10 locations in the Bahamas over a 4-year period. Lobophorolide (1) is structurally unprecedented, yet parts of the molecule are related to tolytoxin, the scytophycins, and the swinholides, macrolides previously isolated from terrestrial cyanobacteria and from marine sponges and gastropods. Until now, compounds of this structural class have not been associated with marine macrophytes. Our findings suggest that seaweeds use targeted antimicrobial chemical defense strategies and that secondary metabolites important in the ecological interactions between marine macroorganisms and microorganisms could be a promising source of novel bioactive compounds.
Effect of concentration and molecular weight on the rheology of hyaluronic acid/bovine calf serum solutions (2009)

Rheological measurements were conducted on hyaluronic acid (HA)/bovine calf serum (BCS) solutions that can be used as analogues of synovial or periprosthetic fluid. The presence of HA affected profoundly the rheological properties of the solutions, with increased concentrations and higher molecular weight of HA leading to higher viscosities as well as more pronounced shear thinning in steady-shear flow. In dynamic oscillatory flow, the elastic character of the solutions became more pronounced and the cross-over frequency decreased upon increasing concentration and molecular weight of HA. The relevance of these results in the context of appropriate selection of a lubricating environment that mimics physiological conditions is discussed.