gebhart/patrepeval huggingface dataset:
Entanglement of Two Superconducting Qubits in a Waveguide Cavity via Monochromatic Two-Photon Excitation (2012)

We report a system where fixed interactions between noncomputational levels make bright the otherwise forbidden two-photon |00}→|11} transition. The system is formed by hand selection and assembly of two discrete component transmon-style superconducting qubits inside a rectangular microwave cavity. The application of a monochromatic drive tuned to this transition induces two-photon Rabi-like oscillations between the ground and doubly excited states via the Bell basis. The system therefore allows all-microwave two-qubit universal control with the same techniques and hardware required for single qubit control. We report Ramsey-like and spin echo sequences with the generated Bell states, and measure a two-qubit gate fidelity of F(g)=90% (unconstrained) and 86% (maximum likelihood estimator).
Therapeutic Effects of Anti-CD115 Monoclonal Antibody in Mouse Cancer Models through Dual Inhibition of Tumor-Associated Macrophages and Osteoclasts (2013)

Tumor progression is promoted by Tumor-Associated Macrophages (TAMs) and metastasis-induced bone destruction by osteoclasts. Both myeloid cell types depend on the CD115-CSF-1 pathway for their differentiation and function. We used 3 different mouse cancer models to study the effects of targeting cancer host myeloid cells with a monoclonal antibody (mAb) capable of blocking CSF-1 binding to murine CD115. In mice bearing sub-cutaneous EL4 tumors, which are CD115-negative, the anti-CD115 mAb depleted F4/80(+) CD163(+) M2-type TAMs and reduced tumor growth, resulting in prolonged survival. In the MMTV-PyMT mouse model, the spontaneous appearance of palpable mammary tumors was delayed when the anti-CD115 mAb was administered before malignant transition and tumors became palpable only after termination of the immunotherapy. When administered to mice already bearing established PyMT tumors, anti-CD115 treatment prolonged their survival and potentiated the effect of chemotherapy with Paclitaxel. As shown by immunohistochemistry, this therapeutic effect correlated with the depletion of F4/80(+)CD163(+) M2-polarized TAMs. In a breast cancer model of bone metastasis, the anti-CD115 mAb potently blocked the differentiation of osteoclasts and their bone destruction activity. This resulted in the inhibition of cancer-induced weight loss. CD115 thus represents a promising target for cancer immunotherapy, since a specific blocking antibody may not only inhibit the growth of a primary tumor through TAM depletion, but also metastasis-induced bone destruction through osteoclast inhibition.
Prohibitin, an antiproliferative protein, is localized to mitochondria (1995)

Prohibitin is a ubiquitously expressed protein with antiproliferative properties. When rat prohibitin tagged with a carboxy-terminal c-Myc epitope was expressed in baby hamster kidney cells the protein was targeted to mitochondria. In immunofluorescence microscopy prohibitin colocalized with a mitochondrial marker E3. Immunoelectron microscopy revealed that prohibitin was associated with the periphery of mitochondria. The amino-terminus of prohibitin shares characteristics of the known mitochondrial import signals, and positioning of the tag at the N-terminus causes accumulation of the protein in the cytoplasm. These findings help to direct functional studies on prohibitin and suggest that a mitochondrial protein may act as a tumor suppressor.
Progress on baculovirus-derived influenza vaccines. (2008)

The baculovirus insect cell production technology allows for rapid vaccine production and is particularly suitable for influenza vaccines where annual adjustment of the composition is required. Recombinant hemagglutinin produced using this technology is safe, immunogenic and effective in preventing cell-culture confirmed influenza in individuals; recombinant neuraminidase may play a role as an additive to improve the currently licensed influenza vaccines. Universal vaccine candidates, such as matrix protein M2 and nucleocapsid protein, are yet to enter the clinic whereas the first pandemic influenza virus-like particle (VLP) vaccine candidate is in clinical development. This review presents an overview of the use of this production system for the development of various influenza vaccine targets, including hemagglutinin, neuraminidase, M2, nucleoprotein and VLPs containing multiple influenza proteins. The development progress and the advantages and disadvantages of each vaccine candidate are discussed.
Immunochemical Studies on Phenylalanyl-tRNA Synthetase fromEscherichia coli (1977)

Antibodies against the alpha and beta subunits of phenylalanyl-tRNA synthetase were fractionated by ion exchange chromatography into different classes and then digested with papain to yield the respective Fab fragments. The preparations obtained were used to investigate (i) whether the alpha and beta polypeptides share any common antigenic determinants and (ii) whether immunological methods are able to resolve the catalytic function of the subunits of this enzyme (or principally of oligomeric enzymes). As to the first problem, immunodiffusion and complement fixation experiments showed that there is no immunological relatedness between the subunits which argues against the existence of sequence homoligies. As to the second question investigated, it was found that any binding of immunoglobulins of Fab fragments to the alpha or the the beta subunit affects enzyme activity either in the direction of activation or inhibition. These results therefore show that the immunological approach is not appropriate for resolving subunit-specific funcitons, possibly as a consequence of conformational changes induced in the enzyme by the binding of the immunoglobulins of Fab fragments.
The synthesis of “stretched‐out” analogs of lumazine, 6,7‐dimethyllumazine and 2‐amino‐5,6,7,8‐tetrahydro‐6,7‐dimethyl‐4‐pteridinone (1981)

Abstract The synthesis of pyrazino[2,3‐ g ]quinazolin‐2,4‐(1 H ,3 H )dione ( 4 ) and its 7,8‐dimethyl derivative ( 5 ), as linear benzo‐separated lumazines, is reported. Also described is the preparation of 2‐amino‐6,7,8,9‐tetrahydro‐7,8‐dimethylpyrazino[2,3‐ g ]quinazolin‐4‐one ( 6 ), as a linear benzo‐separated analog of a synthetic cofactor for phenylalanine hydroxylase. All of the syntheses began with ethyl 2,4,5‐triaminobenzoate ( 8 ) and proceeded through the appropriate derivatives of ethyl 6‐aminoquinoxaline‐7‐carboxylate ( 9, 10 , and 11 ) which were subsequently ring closed to 4, 5 , and 6 .
OKT3 monoclonal antibodies induce interleukin-6 and interleukin-10: a possible cause of lymphoproliferative disorders associated with transplantation (1993)

The risk of posttransplantation lymphoproliferative disorder (PTLD) has increased with the use of new, highly potent immunosuppressive agents. Monoclonal anti-T-cell antibodies such as OKT3 have been associated with a particularly high risk of these frequently fatal Epstein-Barr virus (EBV)-related B-cell neoplasms. OKT3 is a powerful mitogen, raising the possibility that T-cell activation and cytokine release may facilitate the development of PTLD. Interleukin-6 and interleukin-10 have recently been shown to play major roles in B-cell neoplasia in general, and particularly in EBV-induced B-cell transformation and outgrowth. The development of PTLD after treatment with OKT3 might be mediated by the release of those cytokines. On the other hand, OKT3-related PTLD may simply be the result of the profound T-cell depletion induced by the drug, and the mechanisms for lymphomagenesis may be no different than those operative in PTLDs arising in other immunosuppressed patients. A clearer understanding of the relevant mechanisms will require further work with in vivo models of the disease and may have significant implications for the design of new immunosuppressive agents.
IL‐1α secreted by colon cancer cells enhances angiogenesis: The relationship between IL‐1α release and tumor cells' potential for liver metastasis (2009)

Based on these findings, we conclude that colon cancer cell-derived IL-1alpha up-regulates angiogenesis by modulating stromal cells within the tumor cells' microenvironment.
Non-negative matrix factorization for visual coding (2003)

This paper combines linear spun coding and nonnegative matrix factorization into sparse non-negative matrix factorization. In contrast to non-negative matrix factorization, the new model can learn much sparser representation via imposing sparseness constraints explicitly; in contrast to a close model -non-negative sparse coding, the new model can learn parts-based representation via fully multiplicative updates because of adapting a generalized Kullback-Leibler divergence instead of the conventional mean error for approximation error. Experiments on MIT-CBCL training facts data demonstrate the effectiveness of the proposed method.
Dependence of Human Stem Cell Engraftment and Repopulation of NOD/SCID Mice on CXCR4 (1999)

Stem cell homing and repopulation are not well understood. The chemokine stromal cell-derived factor-1 (SDF-1) and its receptor CXCR4 were found to be critical for murine bone marrow engraftment by human severe combined immunodeficient (SCID) repopulating stem cells. Treatment of human cells with antibodies to CXCR4 prevented engraftment. In vitro CXCR4-dependent migration to SDF-1 of CD34+CD38-/low cells correlated with in vivo engraftment and stem cell function. Stem cell factor and interleukin-6 induced CXCR4 expression on CD34+ cells, which potentiated migration to SDF-1 and engraftment in primary and secondary transplanted mice. Thus, up-regulation of CXCR4 expression may be useful for improving engraftment of repopulating stem cells in clinical transplantation.
Identification of a Neuropeptide Hormone That Regulates Sex Pheromone Production in Female Moths (1989)

A pheromone biosynthesis activating neuropeptide (PBAN) hormone that controls sex pheromone production in female moths was identified from the brain-subesophageal ganglion complexes of the adult corn earworm, Heliothis zea. PBAN has 33 amino acid residues and a molecular weight of 3900. Its amino acid sequence has no significant homology with any of the fully characterized peptide hormones. The synthetic peptide, at a dose of between 2 and 4 picomoles, induced production of a normal quantity of sex pheromone in ligated H. zea females. The peptide also induced pheromone production in six other species of moths, thus indicating that this or similar peptides may be responsible for the regulation of pheromone production in moths.
Spin transfer oscillators emitting microwave in zero applied magnetic field (2007)

Using pillar-shaped spin valves with the magnetization of the reference layer being pinned perpendicularly to the easy axis of the free layer, we show that spin-transfer-induced microwave emission can be obtained at exactly zero applied magnetic field and in its vicinity. The frequency tunability (typically 150 MHz/mA), the spectral purity (quality factor up to 280), and the power (up to 5 nV/Hz1/2) of the emission compares well with other spin-transfer oscillators based on spin-valve nanopillars. This ability to get satisfactory microwave emission without needing bulky magnetic field sources may arise from a small nonvanishing field-like term in the current-induced torque. It may be of interest for the design of submicron microwave sources.
Distribution shape of two-dimensional DCT coefficients of natural images (1993)

The univariate distribution of DCT coefficients of natural images is investigated. The probability density function (PDF) of the coefficients is modelled with the generalised Gaussian function (GGF) which includes the Gaussian and the Laplacian PDF as special cases. The shape parameter of the GGF is estimated according to the maximum likelihood principle, χ2 tests of fit showed that GGFs model the distribution of DCT coefficients more accurately than Laplacian PDFs.
Enhanced Green Fluorescent Protein as Selectable Marker of Retroviral-Mediated Gene Transfer in Immature Hematopoietic Bone Marrow Cells (1997)

The further improvement of gene transfer into hematopoietic stem cells and their direct progeny will be greatly facilitated by markers that allow rapid detection and efficient selection of successfully transduced cells. For this purpose, a retroviral vector was designed and tested encoding a recombinant version of the Aequorea victoria green fluorescent protein that is enhanced for high-level expression in mammalian cells (EGFP). Murine cell lines (NIH 3T3, Rat2) and bone marrow cells transduced with this retroviral vector demonstrated a stable green fluorescence signal readily detectable by flow cytometry. Functional analysis of the retrovirally transduced bone marrow cells showed EGFP expression in in vitro clonogenic progenitors (GM-CFU), day 13 colony-forming unit-spleen (CFU-S), and in peripheral blood cells and marrow repopulating cells of transplanted mice. In conjunction with fluorescence-activated cell sorting (FACS) techniques EGFP expression could be used as a marker to select for greater than 95% pure populations of transduced cells and to phenotypically define the transduced cells using antibodies directed against specific cell-surface antigens. Detrimental effects of EGFP expression were not observed: fluorescence intensity appeared to be stable and hematopoietic cell growth was not impaired. The data show the feasibility of using EGFP as a convenient and rapid reporter to monitor retroviral-mediated gene transfer and expression in hematopoietic cells, to select for the genetically modified cells, and to track these cells and their progeny both in vitro and in vivo.
Compact imaging spectrometer combining Fourier transform spectroscopy with a Fabry-Perot interferometer (2009)

An imaging spectrometer based on a Fabry-Perot interferometer is presented. The Fabry-Perot interferometer scans the mirror distance up to contact and the intensity modulated light signal is transformed using a Fourier Transform based algorithm, as the Michelson based Fourier Transform Spectrometers does. The resulting instrument has the advantage of a compact, high numerical aperture, high luminosity hyperspectral imaging device. Theory of operation is described along with one experimental realization and preliminary results.
Transaction support in a log-structured file system (2002)

The design and implementation of a transaction manager embedded in a log-structured file system are described. Measurements indicate that transaction support on a log-structured file system offers a 10% performance improvement over transaction support on a conventional read-optimized file system. When the transaction manager is embedded in the log-structured file system, the resulting performance is comparable to that of a more traditional, user-level system. The performance results also indicate that embedding transactions in the file system need not impact the performance of nontransaction applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Plant-Derived Triterpenoids as Potential Antineoplastic Agents (2003)

Man has relied on plants as a source of medicinal agents for centuries. Today, with the specter of antibiotic resistance, emerging infectious diseases, and cancers, phytochemicals continue to provide new structural leads for the chemotherapeutic industry. A number of triterpenoids have shown promise as antineoplastic agents. Members of the cycloartane, lupane, ursane, oleanane, friedelane (especially quinone methides), dammarane, cucurbitacin, and limonoid triterpenoids, have demonstrated anti-proliferative activity on various cancer cell lines. This review covers the recent developments regarding antineoplastic/cytotoxic triterpenoids, excluding saponins, from higher plants.
Differential Recognition of Surface Proteins inStreptococcus pyogenesby Two Sortase Gene Homologs (2002)

The interaction of Streptococcus pyogenes (group A streptococcus [GAS]) with its human host requires several surface proteins. In this study, we isolated mutations in a gene required for the surface localization of protein F by transposon mutagenesis of the M6 strain JRS4. This gene (srtA) encodes a protein homologous to Staphylococcus aureus sortase, which covalently links proteins containing an LPXTG motif to the cell wall. The GAS srtA mutant was defective in anchoring the LPXTG-containing proteins M6, protein F, ScpA, and GRAB to the cell surface. This phenotype was complemented when a wild-type srtA gene was provided in trans. The surface localization of T6, however, was unaffected by the srtA mutation. The M1 genome sequence contains a second open reading frame with a motif characteristic of sortase proteins. Inactivation of this gene (designated srtB) in strain JRS4 affected the surface localization of T6 but not M6, protein F, ScpA, or GRAB. This phenotype was complemented by srtB in trans. An srtA probe hybridized with DNA from all GAS strains tested (M types 1, 3, 4, 5, 6, 18, 22, and 50 and nontypeable strain 64/14) and from streptococcal groups C and G, while srtB hybridized with DNA from only a few GAS strains. We conclude that srtA and srtB encode sortase enzymes required for anchoring different subsets of proteins to the cell wall. It seems likely that the multiple sortase homologs in the genomes of other gram-positive bacteria have a similar substrate-specific role.
T cell response to grass pollen allergens: Correlation with skin test reactivity and serum IgE levels (1995)

T cell proliferative responses to rye and Bermuda grass pollen allergens have been studied in a series of 51 atopic and 18 non-atopic subjects. Mean T cell responses were higher in the atopic group than in the non-atopic group (P < 0.001), and there was a strong correlation between the magnitude of reaction in the T cell assay and in the skin test (rye P < 0.01, Bermuda P < 0.05). A similar association was shown between T cell reactivity and serum levels of allergen-specific IgE (rye P < 0.05, Bermuda P < 0.05), but no relationship was found between serum allergen-specific IgG levels and any other parameter studied. T cell reactivity was not found in three cord blood samples tested. Discordance between positivity for T cell responses and skin test reactions in some cases might reflect reactivity by T cell subsets that promote IgG antibody or cell-mediated responses without IgE antibody production. A precise knowledge of T cell recognition of grass pollen allergens will provide exciting new prospects for more effective and safer immunotherapy strategies for allergic diseases including asthma.
Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae (2003)

The genome of Chlamydophila caviae (formerly Chlamydia psittaci, GPIC isolate) (1 173 390 nt with a plasmid of 7966 nt) was determined, representing the fourth species with a complete genome sequence from the Chlamydiaceae family of obligate intracellular bacterial pathogens. Of 1009 annotated genes, 798 were conserved in all three other completed Chlamydiaceae genomes. The C.caviae genome contains 68 genes that lack orthologs in any other completed chlamydial genomes, including tryptophan and thiamine biosynthesis determinants and a ribose-phosphate pyrophosphokinase, the product of the prsA gene. Notable amongst these was a novel member of the virulence-associated invasin/intimin family (IIF) of Gram-negative bacteria. Intriguingly, two authentic frameshift mutations in the ORF indicate that this gene is not functional. Many of the unique genes are found in the replication termination region (RTR or plasticity zone), an area of frequent symmetrical inversion events around the replication terminus shown to be a hotspot for genome variation in previous genome sequencing studies. In C.caviae, the RTR includes several loci of particular interest including a large toxin gene and evidence of ancestral insertion(s) of a bacteriophage. This toxin gene, not present in Chlamydia pneumoniae, is a member of the YopT effector family of type III-secreted cysteine proteases. One gene cluster (guaBA-add) in the RTR is much more similar to orthologs in Chlamydia muridarum than those in the phylogenetically closest species C.pneumoniae, suggesting the possibility of horizontal transfer of genes between the rodent-associated Chlamydiae. With most genes observed in the other chlamydial genomes represented, C.caviae provides a good model for the Chlamydiaceae and a point of comparison against the human atherosclerosis-associated C.pneumoniae. This crucial addition to the set of completed Chlamydiaceae genome sequences is enabling dissection of the roles played by niche-specific genes in these important bacterial pathogens.
Stable nuclear transformation of Chlamydomonas reinhardtii by using a C. reinhardtii gene as the selectable marker. (1990)

We have developed a stable nuclear transformation system for the unicellular green alga Chlamydomonas reinhardtii. Transformation was accomplished by introducing the cloned C. reinhardtii oxygen-evolving enhancer protein 1 (OEE1) gene into C. reinhardtii cells by bombardment with DNA-coated tungsten particles. The recipient strain was an OEE1-deficient, nonphotosynthetic, acetate-requiring mutant, which recovered photosynthetic competence after transformation, and was therefore able to grow in the absence of acetate. Analysis of several transformants indicates that transformation has proceeded via second-site integration of the cloned gene, leaving the endogenous mutant gene intact. In genetic crosses of transformants with wild type, both mutant and wild-type phenotypes were recovered, showing that the photosynthetic competence of transformants was due not to reversion of the original locus but rather to expression of the introduced gene. We suggest that the success of the present system is largely due to using a homologous C. reinhardtii gene, leading to stable maintenance and expression of the gene. Transformation with heterologous genes may be problematic because of poor expression due to an unusual codon bias in C. reinhardtii.
Cell-bound complement activation products in systemic lupus erythematosus: comparison with anti-double-stranded DNA and standard complement measurements (2014)

CBCAPS have higher sensitivity than standard complement and anti-dsDNA measurements, and may help with the differential diagnosis of SLE in combination with other autoantibodies.
A new poly-Si TFT with selectively doped channel fabricated by novel excimer laser annealing (2002)

A new excimer laser annealing method, which results in a single grain boundary in the channel of polycrystalline silicon thin film transistor (poly-Si TFT), is proposed. The proposed method employs lateral grain growth through aluminum patterns on an amorphous silicon layer. The aluminum pattern acts as a selective beam mask and a lateral heat sink during the laser irradiation. Poly-Si TFTs fabricated by the proposed ELA method exhibit considerably improved characteristics, such as the high field effect mobility exceeding 240 cm/sup 2//V sec. The turn-off characteristics have also been improved by the field-reducing structure.