gebhart/patrepeval huggingface dataset:
Herpes simplex virus type 1 glycoproteins gB, gC and gD are major targets for CD4 T-lymphocyte cytotoxicity in HLA-DR expressing human epidermal keratinocytes. (1998)

T lymphocytes are the main mediators of the protective immune response in recurrent herpes simplex. Early in the development of recurrent lesions, macrophages and CD4 T lymphocytes predominate in the mononuclear infiltrate surrounding infected epidermal cells. Human epidermal keratinocytes allow herpes simplex virus type 1 (HSV-1) replication and human leukocyte antigen (HLA)-DR is strongly expressed in vivo. In vitro, their pretreatment with IFN-gamma induced HLA-DR expression and partially reversed major histocompatibility complex class I down-regulation by the virus. Mononuclear cell cytotoxicity for these cells was mediated predominantly by CD4 and also by CD8 T cells. Late HSV-1 proteins were the major targets for CD4 CTL, while CD8 CTL predominantly targeted early HSV-1 proteins. Here it is shown that both mononuclear and CD4 CTL consistently recognized the major HSV-1 glycoproteins, gB, gC, gD and gH, using IFN-gamma-pretreated keratinocytes infected with vaccinia virus-HSV glycoprotein recombinants (VvgB, VvgC, VvgD or VvgH). CD4 cytotoxicity was highest for VvgD-infected keratinocytes, followed by VvgB or VvgC and then VvgH in seven patients. CD4 CTL from two of 13 patients also recognized an epitope in the HSV tegument protein VP16, demonstrated by comparing cytotoxicity for the partial deletion mutants RP3 or RP4 and the parental RP1 HSV strain. In summary, the major HSV glycoproteins gB, gC and gD were consistently the major targets for CD4 CTL in VvgB-, VvgC-, VvgD- and VvgH-infected, IFN-gamma-pretreated human epidermal keratinocytes in vitro.
Cloning and expression of the CAMP factor of group B streptococci in Escherichia coli (1988)

The genetic determinant of the CAMP factor from a strain of group B streptococcus (GBS; Streptococcus agalactiae) was cloned in Escherichia coli. Total cell DNA from the GBS strain R268 was used to construct a gene bank with bacteriophage lambda EMBL4 in the E. coli K-12 strain LE392. Recombinant phage plaques were detected by immunoblots by using a specific antiserum raised against purified CAMP factor. Two hybrid phages showing expression of CAMP factor were identified. Subcloning the CAMP gene (cfb) into the high-copy-number vector pUC8 resulted in highly unstable plasmids. Therefore, subcloning was performed with the low-copy-number vector pLG339 resulting in the stable recombinant plasmids pCO61 and pCO62 which lead to expression of CAMP protein first identified by colony immunoblotting. Western blot (immunoblot) analysis revealed a similar CAMP protein pattern in lambda EMBL4 recombinant phage lysates (molecular weight, 22,000 to 24,000) as compared to that obtained from a GBS culture supernatant (molecular weight, 22,000 to 26,000) but a different CAMP protein pattern (molecular weight, 20,000 to 23,000) from lysates of E. coli carrying pCO61 or pCO62. To study the excretion of the CAMP protein we performed a semi-quantitative dot blot analysis of proteins recovered from cell fractions and supernatants of the E. coli recombinant clones. In contrast to GBS R268, where the CAMP factor is readily excreted, the CAMP protein is not excreted in E. coli clones containing pCO61 and pCO62 but is found associated with the cell fractions.
Cell-Free Protein Synthesis Technology in NMR High-Throughput Structure Determination (2009)

This chapter describes the current implementation of the cell-free translation platform developed at the Center for Eukaryotic Structural Genomics (CESG) and practical aspects of the production of stable isotope-labeled eukaryotic proteins for NMR structure determination. Protocols are reported for the use of wheat germ cell-free translation in small-scale screening for the level of total protein expression, the solubility of the expressed protein, and the success in purification as predictive indicators of the likelihood that a protein may be obtained in sufficient quantity and quality to initiate structural studies. In most circumstances, the small-scale reactions also produce sufficient protein to permit bioanalytical and functional characterizations. The protocols incorporate the use of robots specialized for small-scale cell-free translation, large-scale protein production, and automated purification of soluble, His(6)-tagged proteins. The integration of isotopically labeled proteins into the sequence of experiments required for NMR structure determination is outlined, and additional protocols for production of integral membrane proteins in the presence of either detergents or unilamellar liposomes are presented.
HIV-1 and T cell dynamics after interruption of highly active antiretroviral therapy (HAART) in patients with a history of sustained viral suppression (1999)

Identifying the immunologic and virologic consequences of discontinuing antiretroviral therapy in HIV-infected patients is of major importance in developing long-term treatment strategies for patients with HIV-1 infection. We designed a trial to characterize these parameters after interruption of highly active antiretroviral therapy (HAART) in patients who had maintained prolonged viral suppression on antiretroviral drugs. Eighteen patients with CD4(+) T cell counts >/= 350 cells/microliter and viral load below the limits of detection for >/=1 year while on HAART were enrolled prospectively in a trial in which HAART was discontinued. Twelve of these patients had received prior IL-2 therapy and had low frequencies of resting, latently infected CD4 cells. Viral load relapse to >50 copies/ml occurred in all 18 patients independent of prior IL-2 treatment, beginning most commonly during weeks 2-3 after cessation of HAART. The mean relapse rate constant was 0.45 (0.20 log(10) copies) day(-1), which was very similar to the mean viral clearance rate constant after drug resumption of 0.35 (0.15 log(10) copies) day(-1) (P = 0.28). One patient experienced a relapse delay to week 7. All patients except one experienced a relapse burden to >5,000 RNA copies/ml. Ex vivo labeling with BrdUrd showed that CD4 and CD8 cell turnover increased after withdrawal of HAART and correlated with viral load whereas lymphocyte turnover decreased after reinitiation of drug treatment. Virologic relapse occurs rapidly in patients who discontinue suppressive drug therapy, even in patients with a markedly diminished pool of resting, latently infected CD4(+) T cells.
Peak-to-Average Power Ratio Reduction in Multi-User OFDM (2007)

In this paper variants of selected mapping are investigated for different MIMO OFDM scenarios (point-to- point, multiple-access, and broadcast channel). Particular focus is on the broadcast scenario, where transmitter side precoding is mandatory which usually increases peak-to-average power ratio (PAR). The combination of (non-linear) precoding with a selected mapping technique leads to a very high computational complexity because it operates on all carriers. This paper introduces a new PAR reducing method which affects only a subset of carriers and therefore saves complexity. Because PAR reduction is achieved by optimizing the sorting in the precoding scheme, this technique is called selected sorting.
Targeting, internalization, and cytotoxicity of methotrexate-monoclonal anti-stage-specific embryonic antigen-1 antibody conjugates in cultured F-9 teratocarcinoma cells. (1986)

Methotrexate (MTX) conjugates of a monoclonal antibody, anti-SSEA-1, containing an average of 45 mol MTX/mol of immunoglobulin M, were prepared by a carbodiimide coupling reaction. Binding experiments indicate that conjugation does not decrease the affinity of the antibody for its antigen. The conjugate strongly inhibits the growth of SSEA-1-bearing F-9 teratocarcinoma cells, with 50% inhibitory dose of 4.5 nM MTX, which makes it more active than free MTX (50% inhibitory dose of 15 nM). The drug-free antibody is not cytotoxic to F-9 cells at the concentrations used. The high efficacy of the conjugated drug may be due in part to the fact that anti-SSEA-1 antibody is an immunoglobulin M. MTX conjugated to nonspecific immunoglobulin M has little inhibitory effect (50% inhibitory dose of 150 nM). When acting on SSEA-1 negative cells, the two conjugates have only a small but identical effect. Thiamine pyrophosphate, an inhibitor of MTX transport, can prevent the cytotoxicity of the free MTX but not that of the anti-SSEA-1 conjugate. Leupeptin, an inhibitor of lysosomal protease, can partially protect F-9 cells against the antibody conjugate but not against free MTX. These results indicate that the MTX antibody conjugate binds specifically to F-9 cells, and is internalized and intracellularly degraded to release a small molecular active drug. Pretreatments of F-9 cells for 1 h with unlabeled antibody inhibits the subsequent uptake of identical concentration of labeled conjugate. The rate of internalization, however, regains almost normal values within 4 h, indicating a rapid reappearance of free antigenic sites at the cell surface.
Interactive Procedural Street Modeling (sap301) (2001)

This sketch presents a solution to efficiently model the street networks of large urban areas. Parish and Muller [2001] were the first to note that the street network is the key to create a large urban model. While this algorithm created a high quality solution, the method does not allow to incorporate user-control. To address this limitation we provide a rather different alternative to street modeling that allows to integrate a wide variety of user input. The key idea is to use tensor fields to guide the generation of street graphs. A user can interactively edit a street graph by either modifying the underlying tensor field or by changing the graph directly. This allows for efficient modeling, because we can combine high-level and low-level modeling operations, constraints, and procedural methods. The major contributions are as follows: (1) We are the first to introduce a procedural approach to model urban street networks that combines interactive user-guided editing operations and procedural methods. (2) We are introducing a new methodology to graph modeling in general. The idea of tensor-guided graph modeling together with the tight integration of interactive editing and procedural modeling has not been explored previously in related modeling problems, such as modeling of bark, cracks, fracture, or trees.
Simple Silyl Linker for the Solid Phase Organic Synthesis of Aryl- Containing Molecules (1997)

We have designed a simple (dimethylsilyl)propionic acid linker for the solid phase synthesis of aryl-containing organic compounds. The linker is cleaved smoothly with trifluoroacetic acid either in solution or in the vapor phase to release the unsubstituted aryl moiety. Using this linker, we have successfully demonstrated the solid phase synthesis of a test compound which involved alkylation, acylation, and Mitsunobu reactions.
Wing transmission for a micromechanical flying insect (2002)

Flapping wings provide unmatched manoeuvrability for flying microrobots. Recent advances in modelling insect aerodynamics show that adequate wing rotation at the end of the stroke is essential for generating adequate flight forces. We developed a thorax structure using four bar frames combined with an extensible fan-fold wing to provide adequate wing stroke and rotation. Flow measurements on a scale model of the beating wing show promising aerodynamics. Calculations using a simple resonant mechanical circuit model show that piezoelectric actuators can generate sufficient power, force and stroke to drive the wings at 150 Hz.
MOUSE MUTANTS AS MODELS IN ENDOCRINE RESEARCH (1984)

Although Shire (1979) has listed some forty-eight mouse mutants of interest to the endocrinologist, this short review has concentrated upon eleven mutations which have resulted in a significant number of scientific publications over the last 4 or 5 years. The selection of references has had to be limited, but it should be possible easily to expand the list given in this review. Although the proximate cause of none of the eleven mutations has been identified with certainty, the abnormalities of function have included hormone deficiencies and receptor and post-receptor malfunctions. It is perhaps a reflexion on our society in the 1980s, that the bulk of research has concentrated on the obese mouse. However, we still do not know the initial cause of this syndrome. The major disadvantage of the mouse to the hormone assayist lies in the small blood volume and the extreme difficulty in taking serial blood samples over a short period of time. With increased sophistication of assay techniques this may prove less daunting, but is an area where a review of the literature reveals discrepancies between laboratories, and even between data generated by the same laboratory at different times. With regard to the hormone content of endocrine tissues, the way forward for peptide-secreting glands may be in the measurement of mRNA levels for particular hormones. Certainly the methods of recombinant-DNA technology will yield positive information upon the aetiology and expression of some of the syndromes considered above. Organ transplantation is an area in which mutant mice have proved useful, for example gonadal, pituitary and pancreatic tissue transplantation. The grafting of neural tissue in the hpg mouse has added a further dimension to this field of research. The great infrastructure of genetical research in mice has enabled us to breed mutant genes onto different genetic backgrounds. This area of research is one which deserves to expand. The techniques of in vitro fertilization, chimera formation and embryo transfer have been used, in part, in studies on mouse mutants, and should provide technical means for further investigating gene expression. The family of dwarf mutants are ideally suited for research into the expression of genes micro-injected into the fertilized egg (see Charlton & Cox, 1983). As new hormones are isolated and become available for study these mouse mutants may well be useful in delineating physiological functions for natural and pharmacological products.(ABSTRACT TRUNCATED AT 400 WORDS)
Support for continuous media in the DASH system (2002)

The DASH resource model is defined as a basis for reserving and scheduling resources (disk, CPU, network, etc.) involved in end-to-end handling of continuous-media (information flowing continuously over real time i.e. digital audio or digital video) data. The model uses primitives that express work-load characteristics and performance requirements, and defines an algorithm for negotiated reservation of distributed resources. This algorithm is embodied in the session reservation protocol, a backward-compatible extension of the Internet Protocol. Hardware trends and future applications that motivate the DASH resource model are described. The performance requirements for using continuous media and the limitations of existing systems are discussed. The DASH resource model for reserving and scheduling resources is presented. The DASH kernel is briefly described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lexicon of lipid nutrition (IUPAC Technical Report) (2001)

Abstract The intertwining of lipid nutrition with many other disciplines makes contributions from different directions imperative. Chemistry, biochemistry, physiology, food science and technology, industrial processing, and consumer acceptance provide concepts and terms used in lipid nutrition. This document is the product of a working group comprising members of the Committee on the Biological Role of Fatty Acids in Human Nutrition of the International Union of Nutritional Sciences and of the Commission on Oils, Fats, and Derivatives of the International Union of Pure and Applied Chemistry. Shorthand formulas and systematic and trivial names of some biologically important fatty acids are given in Table 1 (saturated fatty acids), Table 2 (monoenoic fatty acids), and Table 3 (polyenoic fatty acids). Fatty acid compositions of foods have been based on the data of the USDA reference that means official grade standards for agriculture of the U.S. Department of Agriculture. Because foods may show large variations in their composition the figures in the annexed tables serve as guidelines only, except those of the Codex alimentarius (Tables 4 and 5), where accepted ranges of the figures are reported. Further, as these standards are in constant revision the reader may contact directly the USDA Agriculture Marketing Service for the last editions of these standards. It is evident that the explanation of the referred terms is a compromise between technological and scientific correctness and the readers' lack of interest in many of the details. But, sometimes a more exhaustive explanation is necessary. Further information then may be found in cross references, although they have been reduced to those of utmost necessity. Terms in the text where cross references are available are printed in boldfaced type. As research and science are progressing and knowledge is increasing, consequently, views on certain nutritional aspects are constantly changing, e.g., the role of essential fatty acids in human nutrition. Therefore, such a work will never be complete, and readers are invited to send their comments and observations to the authors for incorporation into a next edition.
The global impact of glaucoma. (1994)

Although glaucoma is a major global cause of blindness, the lack of a uniform definition of the disease in its different forms makes it difficult to assess its public health impact. By considering the common features of glaucoma, we have analysed available data on the three main forms of the disease: congenital/hereditary glaucoma, primary open-angle, and primary angle-closure glaucoma. A simple model was then developed to estimate the extent of glaucoma on a regional basis, taking into account demographic data, e.g., age distribution, gender and ethnic groups. Overall, the results demonstrate that glaucoma is responsible for approximately 5.2 million blind (15% of the total burden of world blindness).
Eotaxin-2, a Novel CC Chemokine that Is Selective for the Chemokine Receptor CCR3, and Acts Like Eotaxin on Human Eosinophil and Basophil Leukocytes (1997)

A novel human CC chemokine consisting of 78 amino acids and having a molecular mass of 8,778.3 daltons (VVIPSPCCMF FVSKRIPENR VVSYQLSSRS TCLKAGVIFT TKKGQQ SCGD PKQEWVQRYM KNLDAKQKKA SPRARAVA) was isolated together with three minor COOH-terminally truncated variants with 73, 75, and 76 residues. The new chemokine was termed eotaxin-2 because it is functionally very similar to eotaxin. In terms of structure, however, eotaxin and eotaxin-2 are rather distant, they share only 39% identical amino acids and differ almost completely in the NH2-terminal region. Eotaxin-2 induced chemotaxis of eosinophils as well as basophils, with a typically bimodal concentration dependence, and the release of histamine and leukotriene C4 from basophils that had been primed with IL-3. In all assays, eotaxin-2 had the same efficacy as eotaxin, but was somewhat less potent. The migration and the release responses were abrogated in the presence of a monoclonal antibody that selectively blocks the eotaxin receptor, CCR3, indicating that eotaxin-2, like eotaxin, acts exclusively via CCR3. Receptor usage was also studied in desensitization experiments by measuring [Ca2+]i changes in eosinophils. Complete cross-desensitization was observed between eotaxin-2, eotaxin and MCP-4 confirming activation via CCR3. No Ca2+ mobilization was obtained in neutrophils, monocytes and lymphocytes, in agreement with the lack of chemotactic responsiveness. Intradermal injection of eotaxin-2 in a rhesus monkey (100 or 1,000 pmol per site) induced a marked local infiltration of eosinophils, which was most pronounced in the vicinity of postcapillary venules and was comparable to the effect of eotaxin.
Cancer Stem Cells Persist in Many Cancer Cell Lines (2004)

Both stem cells and cancer cells are thought to be capable of unlimited proliferation. Paradoxically, however, some cancers seem to contain stem-like cells (cancer stem cells). To help resolve this paradox, we investigated whether established malignant cell lines, which have been maintained over years in culture, contain a subpopulation of stem cells. We have shown that four cancer cell lines contain a small side population (SP), which, in many normal tissues, is enriched for stem cells of the tissue. We have also shown that SP cells in C6 glioma cell line, but not non-SP cells, can generate both SP and non-SP cells in culture and are largely responsible for the in vivo malignancy of this cell line. We propose that many cancer cell lines contain a minor subpopulation of stem cells that is enriched in a SP, can be maintained indefinitely in culture, and is crucial for their malignancy.
A dynamic voltage scaled microprocessor system (2000)

A microprocessor system is presented in which the supply voltage and clock frequency can be dynamically varied so that the system can deliver high throughput when required while significantly extending battery life during the low speed periods. The system consists of a dc-dc switching regulator, an ARM V4 microprocessor with a 16-kB cache, a bank of 64-kB SRAM ICs, and an I/O interface IC. The four custom chips were fabricated in a standard 0.6-/spl mu/m 3-metal CMOS process. The system can dynamically vary the supply voltage from 1.2 to 3.8 V in less than 70 /spl mu/s. This provides a throughput range of 6-85 MIPS with an energy consumption of 0.54-5.6 mW/MIP yielding an effective energy efficiency as high as 26200 MIPS/W.
Two distinct nuclear transcription factors recognize loop and bulge residues of the HIV-1 TAR RNA hairpin. (1991)

Transcriptional activation by the HIV-1 Tat protein requires specific residues in the hexanucleotide loop and trinucleotide bulge of the TAR RNA stem-loop structure found in the 5'-untranslated leader of all viral transcripts. Tat directly contacts residue U22 in the bulge and is thought to act in concert with cellular factors bound to the loop. We find that HeLa nuclear extracts contain two specific TAR RNA-binding proteins, designated TRP-1 and TRP-2, which compete for binding to the upper portion of the TAR hairpin. Analysis of point mutants in TAR RNA reveals that TRP-1 contacts residues in the loop that are important for trans-activation, whereas TRP-2 contacts the bulge, including the same residue (U22) that is required for the Tat-TAR interaction. Glycerol gradient sedimentation and UV cross-linking experiments indicate that TRP-1 is a large heteromeric complex containing a 185-kD RNA-binding protein, whereas TRP-2 activity derives from a family of 110- to 70-kD proteins. Interestingly, both TRP-1 and TRP-2 promote TAR-dependent transcription in vitro in the presence of Tat, although mixing experiments indicate that each of the three proteins must bind independently to TAR RNA. These findings suggest that the TAR element is recognized by two different nuclear RNA-binding proteins that affect transcriptional regulation by Tat.