gebhart/patrepeval huggingface dataset:
Protection against myocardial dysfunction after a brief ischemic period in transgenic mice expressing inducible heat shock protein 70. (1998)

Brief ischemic periods lead to myocardial dysfunction without myocardial infarction. It has been shown that expression of inducible HSP70 in hearts of transgenic mice leads to decreased infarct size, but it remains unclear if HSP70 can also protect against myocardial dysfunction after brief ischemia. To investigate this question, we developed a mouse model in which regional myocardial function can be measured before and after a temporary ischemic event in vivo. In addition, myocardial function was determined after brief episodes of global ischemia in an isolated Langendorff heart. HSP70-positive mice and transgene negative littermates underwent 8 min of regional myocardial ischemia created by occlusion of the left descending coronary artery, followed by 60 min of reperfusion. This procedure did not result in a myocardial infarction. Regional epicardial strain was used as a sensitive indicator for changes in myocardial function after cardiac ischemia. Maximum principal strain was significantly greater in HSP70-positive mice with 88+/-6% of preischemic values vs. 58+/-6% in transgene-negative mice (P < 0.05). Similarly, in isolated Langendorff perfused hearts of HSP70-positive and transgene-negative littermates exposed to 10 min of global ischemia and 90 min of reperfusion, HSP70 transgenic hearts showed a better-preserved ventricular peak systolic pressure. Thus, we conclude that expression of HSP70 protects against postischemic myocardial dysfunction as shown by better preserved myocardial function.
Test wrapper and test access mechanism co-optimization for system-on-chip (2002)

Test access mechanisms (TAMs) and test wrappers are integral parts of a system-on-chip (SoC) test architecture. Prior research has concentrated on only one aspect of the TAM/wrapper design problem at a time, i.e., either optimizing the TAMs for a set of pre-designed wrappers, or optimizing the wrapper for a given TAM width. In this paper, we address a more general problem, that of carrying out TAM design and wrapper optimization in conjunction. We present an efficient algorithm to construct wrappers that reduce the testing time for cores. Our wrapper design algorithm improves on earlier approaches by also reducing the TAM width required to achieve these lower testing times. We present new mathematical models for TAM optimization that use the core testing time values calculated by our wrapper design algorithm. We further present a new enumerative method for TAM optimization that reduces execution time significantly when the number of TAMs being designed is small. Experimental results are presented for an academic SoC as well as an industrial SoC.
Nonnegative Sparse PCA (2007)

We describe a nonnegative variant of the ”Sparse PCA ” problem. The goal is to create a low dimensional representation from a collection of points which on the one hand maximizes the variance of the projected points and on the other uses only parts of the original coordinates, and thereby creating a sparse representation. What distinguishes our problem from other Sparse PCA formulations is that the projection involves only nonnegative weights of the original coordinates — a desired quality in various fields, including economics, bioinformatics and computer vision. Adding nonnegativity contributes to sparseness, where it enforces a partitioning of the original coordinates among the new axes. We describe a simple yet efficient iterative coordinate-descent type of scheme which converges to a local optimum of our optimization criteria, giving good results on large real world datasets. 1
The Minimal Number of Class II MHC-Antigen Complexes Needed for T Cell Activation (1990)

Major histocompatibility complex (MHC) molecules are exposed to large quantities of self and nonself antigens. It is not known what fraction of MHC molecules needs to be occupied by antigen to induce a T cell response. A quantitative study of naturally processed antigen indicated that T cells could be activated when only 0.03 percent of the total I-Ed purified from antigen-presenting cells (APCs) was occupied with antigen. B cells and macrophages processed hen egg lysozyme (HEL) with different efficiencies, but similar degrees of occupancy were required for T cell stimulation. Higher occupancy was needed for I-Ed-transfected L cells, possibly reflecting the requirement for other accessory molecules for efficient APC-T cell interaction.
Component-based policy deployment for service level differentiation in converging communication networks (2003)

The introduction of service level differentiation in IP networks requires adequate support for defining and administrating network resource usage with regard to QoS, routing and accounting. This paper proposes the abstract switch toolkit (AST), a component-based flexible and scalable framework for defining and administrating IP network control and management. AST is designed for wire-speed switching routers supporting flow detection. With its open and flexible character, AST simplifies the introduction of customized QoS and policy-based routing. A particular advantage of AST is its support for interoperability between public switched and IP-based networks.
Historical overview of the transition to monetary union in Europe (2004)

This paper outlines the organization structure of the European System of Central Banks, comprised of the European Central Bank and the central banks of European Monetary Union member countries. Also outlined are the policy procedures used by the European Central Bank as it implements a common monetary policy for all member countries.
Highly Regio- and Enantioselective Catalytic Hydrogenation of Enamides in Conjugated Diene Systems:  Synthesis and Application of γ,δ-Unsaturated Amino Acids (1998)

An extremely efficient method has been found for the catalytic asymmetric hydrogenation of conjugated α,γ-dienamide esters using the Et-DuPHOS-Rh catalyst system. α,γ-Dienamide ester substrates were prepared via the Suzuki cross-coupling reaction and the Horner−Emmons olefination. Full conversion to the corresponding γ,δ-unsaturated amino acids with very high regio- and enantioselectivity was achieved after short reaction times. This new methodology was applied to the synthesis of the natural product bulgecinine from a prochiral dienamide ester.
Peptide binding to HLA-A2 and HLA-B27 isolated from Escherichia coli. Reconstitution of HLA-A2 and HLA-B27 heavy chain/beta 2-microglobulin complexes requires specific peptides. (1992)

The specificity of peptide binding by human leukocyte antigen (HLA) class I molecules was investigated in a cell-free direct-binding assay. Peptides were assessed for binding to HLA-A2 and HLA-B27 by measuring the formation of heterotrimeric HLA complexes that consisted of iodinated beta 2-microglobulin, HLA heavy chain fragments isolated from the Escherichia coli cytoplasm, and peptide. In this system, no detectable HLA heavy chain-beta 2-microglobulin complexes were formed unless appropriate peptides were intentionally added to the reconstitution solution. Analysis with monoclonal antibodies demonstrated that these heterotrimeric complexes were correctly folded. Five nonhomologous peptides, known to form complexes with HLA-A2 or HLA-B27 from T-cell functional studies, were tested for their capacity to bind to HLA-A2 and HLA-B27 using the reconstitution assay. Four of the peptides bound to the appropriate class I molecule only. One peptide and some (but not all) substitution analogs of it bound to both HLA-A2 and HLA-B27. The effect of peptide length on binding to HLA-B27 was studied, and it was found that the optimal length was 9 or 10 amino acid residues; however, one peptide that bound to HLA-B27 was 15 amino acids long. All peptides that bound to HLA-B27 in the direct-binding assay also competed with antigenic peptides for binding to HLA-B27 on the surface of intact cells, as determined by a standard cytotoxic T-lymphocyte functional assay. Thus, we conclude that HLA-A2 and HLA-B27 bind distinct but partially overlapping sets of peptides and that, at least in vitro, the assembly of HLA heavy chain-beta 2-microglobulin complexes requires specific peptides.
Effects of Poly[d(pGpT)·d(pApC)] and Poly[d(pCpG)·d(pCpG)] Repeats on Homologous Recombination in Somatic Cells (1986)

Sequencing studies have shown that in somatic cells alternating runs of purines and pyrimidines are frequently associated with recombination crossover points. To test whether such sequences actually promote recombination, we have examined the effects of poly[d(pGpT).d(pApC)] and poly[d(pCpG).d(pCpG)] repeats on a homologous recombination event. The parental molecule used in this study, pSVLD, is capable of generating wild-type simian virus 40 DNA via recombination across two 751-base-pair regions of homology and has been described previously (Miller et al., Proc. Natl. Acad. Sci. USA 81:7534-7538, 1984). Single inserts of either a poly[d(pGpT).d(pApC)] repeat or a poly[d(pCpG).d(pCpG)] repeat were positioned adjacent to one region of homology in such a way that the recombination product, wild-type simian virus 40 DNA, could be formed only by recombination within the homologies and not by recombination across the alternating purine-pyrimidine repeats. We have found that upon transfection of test DNAs into simian cells, a poly[d(pCpG).d(pCpG)] repeat enhanced homologous recombination 10- to 15-fold, whereas a poly[d(pGpT).d(pApC)] repeat had less effect. These results are discussed in terms of the features of these repeats that might be responsible for promoting homologous recombination.
Antagonists of CD117 (cKit) signaling inhibit mast cell accumulation in healing skin wounds (2008)

Abstract Mast cells (MCs) have important functional roles in leukocyte recruitment, pain, and wound healing, and increased tissue resident MC function has been associated with several fibrotic diseases. Consequently, the study of MCs in situ can be a direct approach to studying the pharmacodynamic impact of MC‐directed therapeutics in tissues. Here we describe an automated laser scanning cytometry assay that was used to characterize the kinetics of MC accumulation in healing skin wounds and to study the effect of inhibiting CD117 (cKit) signaling. The number of tryptase‐positive MCs approximately doubled 14 days after cutaneous injury in nonhuman primates. Treatment of animals with anti‐CD117 or imatinib mesylate (Gleevec®) reduced MC accumulation at the edge of healing wounds in mice and nonhuman primates, respectively. In translating this MC assay to become a biomarker for human studies, no differences in dermal MC numbers were evident between genders, ages or body mass index from 20 healthy donors. These data suggest that skin is a practical and useful tissue for tracking pharmacodynamic effects of MC‐directed therapies. © 2008 International Society for Advancement of Cytometry
Factors Associated With Establishing a Causal Diagnosis for Children With Cardiomyopathy (2006)

Certain patient characteristics, family history, echocardiographic findings, laboratory testing, and biopsy were associated significantly with establishing a cause of pediatric cardiomyopathy. Early endomyocardial biopsy should be considered strongly for children with dilated cardiomyopathy, for definitive diagnosis of viral myocarditis. Although not widely used, skeletal muscle biopsy may yield a cause for some patients with hypertrophic cardiomyopathy and for patients suspected of having a mitochondrial disorder.
Image registration using a symmetric prior—in three dimensions (2000)

This paper describes a Bayesian method for three-dimensional registration of brain images. A finite element approach is used to obtain a maximum a posteriori estimate of the deformation field at every voxel of a template volume. The priors used by the MAP estimate penalize unlikely deformations and enforce a continuous one-to-one mapping. The deformations are assumed to have some form of symmetry, in that priors describing the probability distribution of the deformations should be identical to those for the inverses (i.e., warping brain A to brain B should not be different probablistically from warping B to A). A gradient descent algorithm is presented for estimating the optimum deformations.
Long-distance Bell-type tests using energy-time entangled photons (1999)

Long-distance Bell-type experiments are presented. The different experimental challenges and their solutions in order to maintain the strong quantum correlations between energy-time entangled photons over more than 10 km are reported and the results analyzed from the point of view of tests of fundamental physics as well as from the more applied side of quantum communication, especially quantum key distribution. Tests using more than one analyzer on each side are also presented.
A Catalogue of Glioblastoma and Brain MicroRNAs Identified by Deep Sequencing (2012)

Glioblastoma is the most common and aggressive primary brain tumor. MicroRNAs (miRNAs) are a set of noncoding RNA of about 20∼22 nt in length and they play regulatory roles such as regulating the expression of proteins. Altered miRNA expression is related to cancers, including glioblastoma. In this report, we used deep sequencing to explore the miRNA profiles of glioblastoma and normal brain tissues. We found 875 and 811 known miRNA and miRNA* in glioblastoma and normal brain tissue, respectively, representing the largest characterization of the miRNAs in GBM so far. 33 of them were upregulated in glioblastoma, including miR-21, which is well known as an oncomir, while 40 of them were downregulated. Using miR-10b, miR-124, miR-433, and miR-92b as examples, we verified the data by quantitative RT-PCR, suggesting that deep sequencing was able to capture the expression profiles of miRNAs. In addition, we found 18 novel miRNA and 16 new miRNA* in glioblastoma and normal brain tissues. This report provides a useful resource for future studies of the roles of miRNAs in the pathogenesis and early detection of glioblastoma.
Deformability of ultrahigh strength 5nm Cu∕Nb nanolayered composites (2008)

In this work, micropillar compression testing has been used to obtain stress-strain curves for sputter-deposited Cu–Nb nanolaminate composites with nominal bilayer thickness of 10nm. In addition to the extremely high flow strength of 2.4GPa, the 5nm Cu∕5nm Nb nanolaminate exhibits significant ductility, in excess of 25% true strain.
Monoclonal antibody PHF-9 recognizes phosphorylated serine 404 of tau protein and labels paired helical filaments (1996)

Paired helical filaments (PHFs) purified from alzheimer's brain consist of hyperphosphorylated microtubule-associated protein tau. In PHF, phosphorylation occurs at ser/thr tau residues. Several of these ser/thr phosphorylation sites lie immediately C-terminal to the tau tubulin binding domain. The C-terminal ser396 to thr413 tau region contains two or more phosphorylated residues and eight possible ser/thr phosphorylation sites. Immunologic studies and mass spectroscopy have identified ser396 as one of the phosphorylation sites but identification of more C-terminal phosphorylated residues has been hampered by the lack of monoclonal antibodies (Mabs) that recognize defined epitopes in this region. We have raised Mabs against PHF purified from Alzheimer's brain. One of these Mabs, PHF-9, showed phosphorylation-dependent binding to purified PHF and recognized a phosphorylated epitope in the C-terminal portion of cyanogen bromide-digested PHF. Epitope mapping studies employing synthetic tau phosphopeptides indicated that PHF-9 labeled a 13-mer tau peptide phosphorylated at ser404 but not the corresponding non-phosphorylated peptide. PHF-9 demonstrated no immunoreactivity with a synthetic peptide phosphorylated at ser396 indicating that the PHF-9 epitope is C-terminal to ser396. In conclusion, the present study describes a Mab, PHF-9, which recognizes phosphorylated ser404 of tau independently of phosphorylated ser396 and indicates that tau ser404 is phosphorylated in PHF.
RNA Binding Properties of the AU-rich Element-binding Recombinant Nup475/TIS11/Tristetraprolin Protein (2002)

Regulation of messenger RNA stability by AU-rich elements is an important means of regulating genes induced by growth factors and cytokines. Nup475 (also known as tristetraprolin, or TIS11) is the prototype for a family of zinc-binding Cys 3 His motif proteins required for proper regulation of tumor necrosis factor mRNA stability in macrophages. We developed an Escherichia coli expression system to produce soluble Nup475 protein in quantity to study its RNA binding properties. Nup475 protein bound a tumor necrosis factor AU-rich element over a broad range of pH and salt concentrations by RNA gel shift. This binding was inhibited by excess zinc metal, providing a potential mechanism for previous reports of zinc stabilization of AU-rich element (ARE) containing messenger RNAs. Immobilized Nup475 protein was used to select its optimal binding site by RNA SELEX and revealed a strong preference for the extended sequence UUAUUUAUU, rather than a simple AUUUA motif. These findings were confirmed by sitedirected mutagenesis of the tumor necrosis factor ARE and RNA gel shifts on c-fos, interferon-, and interferon- ARE fragments. A weaker binding activity toward adenine-rich sites, such as a poly(A) tail RNA fragment, can partially disrupt the Nup475-tumor necrosis factor AU-rich element complex.
Lassa virus activates myeloid dendritic cells but suppresses their ability to stimulate T cells (2018)

Lassa virus (LASV) is responsible for a viral hemorrhagic fever in humans and the death of 3,000 to 5,000 people every year. The immune response to LASV is poorly understood, but type I interferon (IFN-I) and T-cell responses appear to be critical for the host. We studied the response of myeloid dendritic cells (mDC) to LASV, as mDCs are involved in both IFN-I production and T-cell activation. We compared the response of primary human mDCs to LASV and Mopeia virus (MOPV), which is similar to LASV, but non-pathogenic. We showed that mDCs produced substantial amounts of IFN-I in response to both LASV and MOPV. However, only MOPV-infected mDCs were able to activate T cells. More surprisingly, coculture with T cells completely inhibited the activation of LASV-infected mDCs. These differences between LASV and MOPV were mostly due to the LASV nucleoprotein, which has major immunosuppressive properties, but the glycoprotein was also involved. Overall, these results suggest that mDCs may be important for the global response to LASV and play a role in the outcome of Lassa fever.
Surface-Nitrided Nickel with Bifunctional Structure As Low-Cost Counter Electrode for Dye-Sensitized Solar Cells (2010)

Surface-nitrided nickel foil and particle films were prepared through the nitridation of metallic nickel foil and particle films in ammonia atmosphere. The microstructure of the obtained surface nitrided nickel foil and particle films was characterized by scanning electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. It is shown that only a thin nitrided layer can be formed on the surface of the metallic nickel after the nitridation, while the bulk phase still remains the stable metallic nickel structure. Surface-nitrided nickel film is directly investigated as a low cost counter electrode material for dye-sensitized solar cells. Clearly, the surface-nitrided nickel layer shows high electrocatalytic activity for reduction of triiodide, and the bulk metallic phase provides good electrical conductivity. Correspondingly, the assembly of these two important functions makes surface-nitrided nickel present an excellent photovoltaic performance of dye-sensitized solar cells (DSSCs), competing with the conventional Pt counter electrode. Therefore, the surface-nitrided Ni with a bifunctional structure as presented in this work is a potential low-cost alternative to the expensive noble metal Pt in future applications of dye-sensitized solar cells.
Influence of substrate temperature and deposition rate on structure of thick sputtered Cu coatings (1975)

Thick [1–10 mil (25.4–254.0 μm)] OFHC copper coatings were deposited on copper, tantalum, and stainless-steel substrates maintained at temperatures (T) in the 50 °–950 °C range, at rates of from 200 to 18 000 Å/min, using primarily hollow and also post-type cathode sputtering apparatuses at argon pressures of 1 and 30 mTorr. Coating structures were examined by preparing metallographic cross sections. Surface topographies and fracture cross sections were examined by scanning electron microscopy. Crystallographic orientations were determined by x-ray diffraction. No significant deposition rate influence was found on the low-temperature structure zones reported previously [J. A. Thornton, J. Vac. Sci. Technol. 11, 666 (1974)] or on the columnar nature of coatings formed at elevated T. Truly equiaxed grain structures were generally not observed with hollow cathodes. Annealing twins were found within the grains for T≳350 °C. Evidence of extensive recrystallization and grain growth was seen for T∠900 °C. Coatings deposited at low rates and T≳400 °C on Cu substrates exhibited epitaxial effects; those on dissimilar substrates showed evidence of agglomeration.
Cytochrome P4502D6193–212: A New Immunodominant Epitope and Target of Virus/Self Cross-Reactivity in Liver Kidney Microsomal Autoantibody Type 1-Positive Liver Disease (2003)

Cytochrome P4502D6 (CYP2D6), target of liver kidney microsomal autoantibody type 1 (LKM1), characterizes autoimmune hepatitis type 2 (AIH2) but is also found in patients with chronic hepatitis C virus (HCV) infection. To provide a complete linear epitope B cell map of CYP2D6, we tested peptides spanning the entire sequence of CYP2D6. In addition to confirming previously described antigenic sites, we identified four new epitopes (193-212, 238-257, 268-287, and 478-497). CYP2D6(193-212) is immunodominant and was the target of 12 of 13 (93%) patients with AIH2 and 5 of 10 (50%) HCV/LKM1-positive patients. Because LKM1 is present in both AIH2 and a viral infection, we tested whether Abs to CYP2D6(193-212) arise through cross-reactive immunity between virus and self. We identified a hexameric sequence "RLLDLA" sharing 5 of 6 aa with "RLLDLS" of HCV(2985-2990) and all 6 aa with CMV(130-135). Of 17 CYP2D6(193-212)-reactive sera, 11 (7 AIH and 4 HCV) reacted by ELISA with the HCV homologue, 8 (5 AIH and 3 HCV) with the CMV homologue, and 8 (5 AIH and 3 HCV) showed double reactivity. Autoantibody binding to CYP2D6(193-212) was inhibited by preincubation with HCV(2977-2996) or CMV(121-140). Recombinant HCV-nonstructural protein 5 and CMV-UL98 proteins also inhibited Ab binding to CYP2D6(193-212). Affinity-purified CYP2D6(193-212)-specific Ab inhibited the metabolic activity of CYP2D6. The demonstrated similarity and cross-reactivity between CYP2D6(193-212) and two unrelated viruses suggests that multiple exposure to viruses mimicking self may represent an important pathway to the development of autoimmunity.
Cryopreservation of biopsied embryos at the blastocyst stage (2006)

Neither the survival rate nor the subsequent development and chances of implantation, differed between embryos frozen at the blastocyst stage following biopsy and those frozen intact.