gebhart/patrepeval huggingface dataset:
Protein Involvement in Transmembrane Lipid Asymmetry (1992)

Transmembrane asymmetry has been extensively studied in eukaryotic cells. It is as yet only clearly demonstrated in the plasma membrane of a few cells. Subcellular organelles have evidence of lipid asymmetry, but very little consistent quantitative data exist. Proteins involved in transmembrane passage of lipids comprise enzymes of lipid metabolism and also the so-called phospholipid flippases that are either passive or active putative lipid transporters. The aminophospholipid translocase that pumps amino-phospholipids from the outer to the inner monolayer of the plasma membrane of eukaryotes is a Mg(2+)-ATP dependent protein with a high lipid selectivity. Lipid asymmetry provides an asymmetrical environment for membrane enzymes. Thus, PS (and PE) reorientation could be a way of controlling or triggering specific enzymes. Also, the asymmetrical distribution of phospholipids most likely determines the fusion-competent membranes and/or which sides of membranes should fuse. Finally, the lipid pump as well as all enzymes responsible for the net transmembrane flux of phospholipids may provide the driving force for membrane bending, notably during the formation of endocytic vesicles. Clearly, real progress in this area will be made only if the proteins of the flippase family are purified and antibodies obtained that will permit the recognition and localization of these proteins in various cells. Also, specific inhibitors as well as mutants would allow one to infer more directly what are the real functions of these proteins. At a late stage, the protein purification will eventually permit speculation on the mechanism of action of a pump that must transport simultaneously hydrophilic and hydrophobic groups through a membrane.
Analysis of the Hump Characteristics in Poly-Si Thin Film Transistor (2006)

To reduce the hump characteristic which is one of the critical issues in poly-Si TFT, we focus on crowding of gate fringing field at channel edge and suggest new modified structure of channel edge. Using dry etching process, poly-Si layer of channel edge is partially removed and the steep profile of channel edge is made into a step profile to decrease the number of carriers from active area. The edge step active (ESA) structure we proposed has a positive effect on removing the hump characteristics.
Azithromycin for the Secondary Prevention of Coronary Events (2005)

A one-year course of weekly azithromycin did not alter the risk of cardiac events among patients with stable coronary artery disease.
Numerical calculation of equivalent grid block permeability tensors for heterogeneous porous media (1991)

A numerical procedure for the determination of equivalent grid block permeability tensors for heterogeneous porous media is presented. The method entails solution of the fine scale pressure equation subject to periodic boundary conditions to yield, upon appropriate averaging of the fine scale velocity field, the coarse scale or equivalent grid block permeability. When the region over which this coarse scale permeability is computed constitutes a representative elementary volume (REV), the resulting equivalent permeability may be interpreted as the effective permeability of the region. Solution of the pressure equation on the fine scale is accomplished through the application of an accurate triangle‐based finite element numerical procedure, which allows for the modeling of geometrically complex features. The specification of periodic boundary conditions is shown to yield symmetric, positive definite equivalent permeability tensors in all cases. The method is verified through application to a periodic model problem and is then applied to the scale up of areal and cross sections with fractally generated permeability fields. The applicability and limitations of the method for these more general heterogeneity fields are discussed.
SOD2 Functions Downstream of Sch9 to Extend Longevity in Yeast (2003)

Signal transduction pathways inactivated during periods of starvation are implicated in the regulation of longevity in organisms ranging from yeast to mammals, but the mechanisms responsible for life-span extension are poorly understood. Chronological life-span extension in S. cerevisiae cyr1 and sch9 mutants is mediated by the stress-resistance proteins Msn2/Msn4 and Rim15. Here we show that mitochondrial superoxide dismutase (Sod2) is required for survival extension in yeast. Deletion of SOD2 abolishes life-span extension in sch9Delta mutants and decreases survival in cyr1:mTn mutants. The overexpression of Sods--mitochondrial Sod2 and cytosolic CuZnSod (Sod1)--delays the age-dependent reversible inactivation of mitochondrial aconitase, a superoxide-sensitive enzyme, and extends survival by 30%. Deletion of the RAS2 gene, which functions upstream of CYR1, also doubles the mean life span by a mechanism that requires Msn2/4 and Sod2. These findings link mutations that extend chronological life span in S. cerevisiae to superoxide dismutases and suggest that the induction of other stress-resistance genes regulated by Msn2/4 and Rim15 is required for maximum longevity extension.
Competition between ponderomotive and thermal forces in short-scale-length laser plasmas (1992)

Interactions of intense 400-fs laser pulses with a solid target are studied with time-integrated and time-resolved measurements. The latter are accomplished by means of a pump and probe experiment, in which the motion of the critical surface is measured with 250-fs resolution. It is found that when the average electron quiver energy (${\mathit{mv}}_{\mathrm{os}}^{2}$/2) becomes comparable to the electron thermal energy (${\mathit{kT}}_{\mathit{e}}$), the ponderomotive force of the high-intensity laser significantly reduces the thermal expansion of a laser plasma. This study is performed in an interesting regime not easily accessible with longer pulse lasers, in which the electron density scale length during the laser pulse was much less than the laser wavelength.
Protection of cultured human monocytes from lymphokine-activated killer-mediated lysis by IFN-gamma. (1988)

We have recently reported that IL 2-activated killer (LAK) cells are capable of lysing cultured human monocytes. In an effort to protect autologous monocytes from lysis, we treated monolayer cultures of adherent PBMC with various doses of human rIFN-gamma and assessed their susceptibility to LAK cells. IFN-gamma was shown to lessen the sensitivity of monocytes to lysis in a dose-dependent manner. Similar treatment of FMEX, an NK-resistant melanoma tumor cell line, with IFN-gamma did not affect its susceptibility to LAK lysis. Kinetic studies demonstrated that as little as 2 h incubation with IFN-gamma was sufficient for the protective effects to take effect. Additionally, monocytes that were pulsed with IFN-gamma for 2 h, washed, and then cultured in medium alone retained their resistance to lysis for at least 3 days. Cold target inhibition studies showed that IFN-treated and untreated monocytes could effectively compete with each other for binding sites on LAK cells. Furthermore, binding studies demonstrated that there was no significant difference between the number of conjugates formed by using either IFN-treated or untreated monocytes. This indicates that resistance to lysis induced by IFN treatment affects a post-binding event and not an initial recognition signal. From these studies, it was apparent that treatment of monocytes with IFN-gamma lessened their sensitivity to LAK-mediated lysis. Thus, it may be possible through a specific sequence of IFN-gamma and IL-2 treatment that LAK activity could be manipulated against some tumor cells, but not normal cells, to abrogate some of the toxicity seen with this type of cancer therapy.
Measurement of Sex Steroid Hormones in Breast Adipocytes: Methods and Implications (2008)

These data support the feasibility of measuring steroid hormone concentrations in breast adipocytes in epidemiologic studies. Future investigations that include the measurement of hormones in the breast microenvironment may have value in understanding breast carcinogenesis, developing prevention strategies, and assessing hormonal treatments.
Explaining Recent Changes in Home Prices (2005)

The increase in housing prices in the past ten years can largely be explained by falling mortgage interest rates and changes in household income. This article offers some projections of what might happen to housing prices if mortgage rates increase.
Deletion of Fcγ Receptor IIB Renders H-2b Mice Susceptible to Collagen-induced Arthritis (1999)

Autoimmune diseases, like rheumatoid arthritis, result from a dysregulation of the immune response culminating in hyperactivation of effector cells leading to immune-mediated injury. To maintain an appropriate immune response and prevent the emergence of autoimmune disease, activation signals must be regulated by inhibitory pathways. Biochemical and genetic studies indicate that the type IIB low-affinity receptor for immunoglobulin (Ig)G (FcgammaRIIB) inhibits cellular activation triggered through antibody or immune complexes and may be an important component in preventing the emergence of autoimmunity. To investigate the role of FcgammaRIIB in the development of type II collagen (CII)-induced arthritis (CIA), a model for rheumatoid arthritis in humans, we have examined its contribution in determining the susceptibility to CIA in the nonpermissive H-2(b) haplotype. H-2(b) mice immunized with bovine CII do not develop appreciable disease. In contrast, immunization of the FcgammaRIIB-deficient, H-2(b) mice with bovine CII induced CIA at an incidence of 42.2%. The maximal arthritis index of the FcgammaRIIB-deficient mice developing CIA (6.9 +/- 3.6) was comparable to that of DBA/1 mice (8.6 +/- 1.9), an H-2(q) strain susceptible for CIA induction. IgG1, IgG2a, and IgG2b antibody responses against CII were elevated in the FcgammaRIIB-deficient animals, especially in those mice showing arthritis, but less pronounced than DBA/1 mice. Histological examinations of the arthritic paws from FcgammaRIIB-deficient mice revealed that cartilage was destroyed and bone was focally eroded in association with marked lymphocyte and monocyte/macrophage infiltration, very similar to the pathologic findings observed in DBA/1 mice. These results indicate that a nonpermissive H-2(b) haplotype can be rendered permissive to CIA induction through deletion of FcgammaRIIB, suggesting that FcgammaRIIB plays a critical role in suppressing the induction of CIA.
Oncogenic K‐Ras decouples glucose and glutamine metabolism to support cancer cell growth (2011)

Oncogenes such as K-ras mediate cellular and metabolic transformation during tumorigenesis. To analyze K-Ras-dependent metabolic alterations, we employed ¹³C metabolic flux analysis (MFA), non-targeted tracer fate detection (NTFD) of ¹⁵N-labeled glutamine, and transcriptomic profiling in mouse fibroblast and human carcinoma cell lines. Stable isotope-labeled glucose and glutamine tracers and computational determination of intracellular fluxes indicated that cells expressing oncogenic K-Ras exhibited enhanced glycolytic activity, decreased oxidative flux through the tricarboxylic acid (TCA) cycle, and increased utilization of glutamine for anabolic synthesis. Surprisingly, a non-canonical labeling of TCA cycle-associated metabolites was detected in both transformed cell lines. Transcriptional profiling detected elevated expression of several genes associated with glycolysis, glutamine metabolism, and nucleotide biosynthesis upon transformation with oncogenic K-Ras. Chemical perturbation of enzymes along these pathways further supports the decoupling of glycolysis and TCA metabolism, with glutamine supplying increased carbon to drive the TCA cycle. These results provide evidence for a role of oncogenic K-Ras in the metabolic reprogramming of cancer cells.
Molecular dissection of membrane-transport proteins: mass spectrometry and sequence determination of the galactose–H+ symport protein, GalP, of Escherichia coli and quantitative assay of the incorporation of [ring-2-13C]histidine and 15NH3 (2002)

The molecular mass of the galactose-H(+) symport protein GalP, as its histidine-tagged derivative GalP(His)(6), has been determined by electrospray MS (ESI-MS) with an error of <0.02%. One methionine residue, predicted to be present from the DNA sequence, was deduced to be absent. This is a significant advance on the estimation of the molecular masses of membrane-transport proteins by SDS/PAGE, where there is a consistent under-estimation of the true molecular mass due to anomalous electrophoretic migration. Addition of a size-exclusion chromatography step after Ni(2+)-nitrilotriacetate affinity purification was essential to obtain GalP(His)(6) suitable for ESI-MS. Controlled trypsin, trypsin+chymotrypsin and CNBr digestion of the protein yielded peptide fragments suitable for ESI-MS and tandem MS analysis, and accurate mass determination of the derived fragments resulted in identification of 82% of the GalP(His)(6) protein. Tandem MS analysis of selected peptides then afforded 49% of the actual amino acid sequence of the protein; the absence of the N-terminal methionine was confirmed. Matrix-assisted laser-desorption ionization MS allowed identification of one peptide that was not detected by ESI-MS. All the protein/peptide mass and sequence determinations were in accord with the predictions of amino acid sequence deduced from the DNA sequence of the galP gene. [ring-2-(13)C]Histidine was incorporated into GalP(His)(6) in vivo, and ESI-MS analysis enabled the measurement of a high (80%) and specific incorporation of label into the histidine residues in the protein. MS could also be used to confirm the labelling of the protein by (15)NH(3) (93% enrichment) and [(19)F]tryptophan (83% enrichment). Such MS measurements will serve in the future analysis of the structures of membrane-transport proteins by NMR, and of their topology by indirect techniques.
Systematic review of antimicrobial treatments for diabetic foot ulcers (2006)

The evidence is too weak to recommend any particular antimicrobial agent. Large studies are needed of the effectiveness and cost-effectiveness of antimicrobial interventions.
High mobility transparent thin-film transistors with amorphous zinc tin oxide channel layer (2004)

Transparent thin-film transistors (TTFTs) with an amorphous zinc tin oxide channel layer formed via rf magnetron sputter deposition are demonstrated. Field-effect mobilities of 5–15 and 20–50cm2V−1s−1 are obtained for devices post-deposition annealed at 300 and 600°C, respectively. TTFTs processed at 300 and 600°C yield devices with turn-on voltage of 0–15 and −5–5V, respectively. Under both processing conditions, a drain current on-to-off ratio greater than 107 is obtained. Zinc tin oxide is one example of a new class of high performance TTFT channel materials involving amorphous oxides composed of heavy-metal cations with (n−1)d10ns0 (n⩾4) electronic configurations.
In vitro synthesis of the iron–molybdenum cofactor of nitrogenase from iron, sulfur, molybdenum, and homocitrate using purified proteins (2007)

Biological nitrogen fixation, the conversion of atmospheric N2 to NH3, is an essential process in the global biogeochemical cycle of nitrogen that supports life on Earth. Most of the biological nitrogen fixation is catalyzed by the molybdenum nitrogenase, which contains at its active site one of the most complex metal cofactors known to date, the iron-molybdenum cofactor (FeMo-co). FeMo-co is composed of 7Fe, 9S, Mo, R-homocitrate, and one unidentified light atom. Here we demonstrate the complete in vitro synthesis of FeMo-co from Fe(2+), S(2-), MoO4(2-), and R-homocitrate using only purified Nif proteins. This synthesis provides direct biochemical support to the current model of FeMo-co biosynthesis. A minimal in vitro system, containing NifB, NifEN, and NifH proteins, together with Fe(2+), S(2-), MoO4(2-), R-homocitrate, S-adenosyl methionine, and Mg-ATP, is sufficient for the synthesis of FeMo-co and the activation of apo-dinitrogenase under anaerobic-reducing conditions. This in vitro system also provides a biochemical approach to further study the function of accessory proteins involved in nitrogenase maturation (as shown here for NifX and NafY). The significance of these findings in the understanding of the complete FeMo-co biosynthetic pathway and in the study of other complex Fe-S cluster biosyntheses is discussed.
Importance of Cellular Microenvironment and Circulatory Dynamics in B Cell Immunotherapy (2005)

B cell immunotherapy has emerged as a mainstay in the treatment of lymphomas and autoimmune diseases. Although the microenvironment has recently been demonstrated to play critical roles in B cell homeostasis, its contribution to immunotherapy is unknown. To analyze the in vivo factors that regulate mechanisms involved in B cell immunotherapy, we used a murine model for human CD20 (hCD20) expression in which treatment of hCD20(+) mice with anti-hCD20 mAbs mimics B cell depletion observed in humans. We demonstrate in this study that factors derived from the microenvironment, including signals from the B cell-activating factor belonging to the TNF family/BLyS survival factor, integrin-regulated homeostasis, and circulatory dynamics of B cells define distinct in vivo mechanism(s) and sensitivities of cells in anti-hCD20 mAb-directed therapies. These findings provide new insights into the mechanisms of immunotherapy and define new opportunities in the treatment of cancers and autoimmune diseases.
The Differential Benefits Of Aerobic Fitness For Cognitive Performance As A Function Of ApoE Genotype (2005)

The apolipoprotein E epsilon 4 (ApoE-ε4) allele is a common susceptibility gene for late-onset cognitive decline and Alzheimer's dementia (AD). However, since this gene is neither necessary nor sufficient for the development of these problems, it would be beneficial to identify risk modifiers, some of which may interact with ApoE-ε4 allele in the prediction of cognitive outcomes. Purpose: Therefore, the purpose of this study was to examine the effects of ApoE-ε4 gene dose, aerobic fitness (VO2max), and their interaction on cognitive measures hypothesized to be sensitive to the interaction. Methods: Data were collected from 85 cognitively normal older women (51–77 yrs, M = 61.8 yrs). Participants provided blood samples for ApoE genotypes, understood that they would receive no information about their ApoE genotypes, completed a battery of clinical ratings and neuropsychological tests, and performed a VO2max test. The sample included 7 ε4 homozygotes, 25 ε4 heterozygotes, and 53 ε4 non-carriers. Hierarchical regression analyses were conducted with depression, years of education, time between cognitive and fitness tests, and age entered first, followed by main effects for VO2max and ApoE-ε4 gene dose, followed by the interaction terms for VO2max by ApoE-ε4. Results: After controlling for main effects, the interaction of ApoE-ε4 gene dose by aerobic fitness predicted a significant (p < .05) percentage of the variance in performance (R2 = 7–9%) on several subscales of the Wechsler Adult Intelligence Scale (Perceptual Organization, Information, Block Design, Digit Symbol Substitution) and on the Complex Figures Test recall scale. Examination of the results indicated that the findings were consistent across all cognitive measures and were such that VO2max was positively related to cognitive performance for the ε4 homozygotes and was generally not related to performance for the ε4 heterozygotes or the ε4 non-carriers. Conclusion: These findings suggest that aerobic fitness is associated with better cognitive performance in homozygous carriers of a common AD susceptibility gene. Larger samples, our ongoing longitudinal assessments, the conductance of true-experimental studies, and the study of persons with other AD risk factors are needed to further demonstrate the protective effects of aerobic fitness on the subsequent development of cognitive decline and probable AD in persons at higher risk for these problems. Supported by NIA grants 1-R03AG022621 and P30 AG19610, NIMH grant RO1 MH057899, the Alzheimer's Association grants IIRG-98-068 and IIRG-98-078, the Arizona Alzheimer's Research Center, and the Arizona State University Stress Center.
Broadly-Tunable Resonant Cavity Light-Emitting Diode (1995)

Microelectromechanical wavelength tuning is demonstrated for the first time in a resonant-cavity light-emitting diode. The device utilizes a deformable-membrane top mirror suspended by an air gap above a diode-active region and bottom mirror. Applied membrane-substrate bias produces an electrostatic force which reduces the air-gap thickness, and therefore, the resonant wavelength. We report broad tunability of nearly 40 nm and spectral linewidths as narrow as 1.9 nm (2.6 meV) for operation near 950 nm. >
The H.264/MPEG4 advanced video coding standard and its applications (2006)

H.264/MPEG4-AVC is the latest video coding standard of the ITU-T video coding experts group (VCEG) and the ISO/IEC moving picture experts group (MPEG). H.264/MPEG4-AVC has recently become the most widely accepted video coding standard since the deployment of MPEG2 at the dawn of digital television, and it may soon overtake MPEG2 in common use. It covers all common video applications ranging from mobile services and videoconferencing to IPTV, HDTV, and HD video storage. This article discusses the technology behind the new H.264/MPEG4-AVC standard, focusing on the main distinct features of its core coding technology and its first set of extensions, known as the fidelity range extensions (FRExt). In addition, this article also discusses the current status of adoption and deployment of the new standard in various application areas
Linear techniques of phase measurement by femtosecond spectral interferometry for applications in spectroscopy (1995)

Although nonlinear methods can provide only the amplitude and the phase of an isolated ultrashort pulse, linear techniques can yield such measurements with a much better sensitivity and reliability when a reference pulse is available. We demonstrate two such methods, dual-quadrature spectral interferometry and Fourier-transform spectral interferometry. These techniques are simple to implement, very sensitive, and provide a complete measurement of the complex electric field, E(ω), as a continuous function of frequency.
Arthritis induced by a T-lymphocyte clone that responds to Mycobacterium tuberculosis and to cartilage proteoglycans. (1985)

Adjuvant arthritis characterized by chronic inflammation of the joints of rats is induced by immunization to Mycobacterium tuberculosis. To learn how autoimmune arthritis may be caused by a microbial antigen, we isolated a T-lymphocyte clone specific for M. tuberculosis antigens that was strongly arthritogenic. We now report that the clone recognized, in addition to M. tuberculosis antigens, antigens present in human synovial fluid, medium of chondrocyte cultures, and proteoglycans purified from cartilage. These observations indicate that the target antigen for the arthritogenic clone resides in the proteoglycan component of cartilage. As this arthritogenic clone shows specificity for both a M. tuberculosis antigen and a cartilage constituent we conclude that disease is probably caused by antigenic cross-reactivity. Thus, an autoimmune disease may be triggered by structural mimicry between antigens in the environment and self-antigens in the individual.