gebhart/patrepeval huggingface dataset:
Evaluation of Pad Groove Designs under Reduced Slurry Flow Rate Conditions during Copper CMP (2008)

The main objective of this investigation is to verify if "smart" groove designs can increase slurry utilization, by controlling the amount of slurry transferred from the pad grooves to the land area-wafer interface, resulting in process optimization. Based on previous studies concerning Logarithmic-Spiral as well as Concentric Slanted grooves, two groove designs were selected to be evaluated and compared to the popular industrial groove design (concentric grooves) under reduced slurry flow rate conditions during copper polishing. The effect of several process parameters were investigated, including pad groove design, applied wafer pressure, and slurry flow rate. Theoretical examination of the experimental data was performed by applying a three-step copper RR model, in order to establish the effect of groove designs on the chemical and mechanical mechanisms present during copper chemical mechanical polishing (CMP).
Erythropoietin secretion and physiological effect in mouse after intramuscular plasmid DNA electrotransfer (1999)

In vivo electrotransfer appears to be a convenient method for obtaining high erythropoietin expression in mice, and it could also be used for the expression of other secreted therapeutic proteins.
A Critical Role for Interleukin 18 in Primary and Memory Effector Responses to Listeria monocytogenes That Extends Beyond Its Effects on Interferon γ Production (2001)

The stimulation of interferon (IFN)-gamma by interleukin (IL)-12 has been shown to provide protection from intracellular pathogens such as Listeria monocytogenes. Tumor necrosis factor (TNF) is also a major player in the resolution of Listeria infections and is suggested to have more global effects than can be explained by the induction of IFN-gamma alone. Since IL-18 synergizes with IL-12 to induce IFN-gamma production by natural killer and T helper (Th)1 cells, we determined its role in responses to Listeria. IL-18 appeared to be even more potent than either IL-12 or IFN-gamma for protection against this pathogen and IL-18 enhanced bacterial clearance in the complete absence of IFN-gamma. Indeed IL-18 was comparable to TNF in its ability to resolve the infection and showed a lowered protective capacity in the absence of TNF. Moreover, IL-18 induced macrophages to secrete both TNF and nitric oxide after a Listeria infection. IL-18 was also essential for optimal IFN-gamma production by antigen-specific T cells. Therefore, IL-18 operates via its effects on both the innate immune response, including macrophages, as well as on Th1 cells, to protect against Listeria.
Optimisation of processing and properties of medical grade Nitinol wire (2000)

AbstractThe purpose of this paper is to review the current processing and resultant properties of standard Nitinol wire for guide-wire applications. Optimised Ti-50.8at%Ni wire was manufactured according to industry standards by precise control of the composition, cold work and continuous strain-age annealing. Mechanical properties of this wire are reported from -100°C to 200°C to demonstrate the effects of test temperature. Within the ‘superelastic window’ the plateau stresses are linearly related to test temperature. Additional ageing treatments can be used as a tool to fine-tune transformation temperatures and mechanical properties. A review of the fatigue properties of thermomechanically-treated Nitinol wire shows that they are affected by test temperature, stress and strain.Key Words: Nitinolshape-memorysuperelasticitymechanical propertiesageingfatigue
Semi-automated data processing of hydrogen exchange mass spectra using HX-Express (2006)

A Microsoft Excel utility, HX-Express, that significantly accelerates the analysis of hydrogen exchange mass spectrometry data is described. HX-Express generates deuterium uptake and peak width plots from peaks in mass spectral data. Data analysis is intentionally semi-automated, requiring that the user find the peaks to be analyzed. The peaks are entered in the form of x, y lists of m/z versus intensity or can be directly imported from Waters MassLynx software. Analysis of data with HX-Express provides the same results as manual data processing but is substantially faster. In addition to speed, HX-Express provides and preserves visual and numeric displays of the analysis process for quality control.
How Viruses Enter Animal Cells (2004)

Viruses replicate within living cells and use the cellular machinery for the synthesis of their genome and other components. To gain access, they have evolved a variety of elegant mechanisms to deliver their genes and accessory proteins into the host cell. Many animal viruses take advantage of endocytic pathways and rely on the cell to guide them through a complex entry and uncoating program. In the dialogue between the cell and the intruder, the cell provides critical cues that allow the virus to undergo molecular transformations that lead to successful internalization, intra-cellular transport, and uncoating.
Detection of Intact Influenza Viruses using Biotinylated Biantennary S-Sialosides (2008)

We report the modular synthesis of robust, biotinylated biantennary sialylglycoconjugates and their ability to differentiate between two type A influenza strains. This is the first demonstration of glycoconjugate-based discriminatory capture and detection of two strains of intact influenza virus, in the presence of the innate enzymatic activity of viral neuraminidases. We also demonstrate a "carboassay" using glycoconjugates as capture and reporter elements, which therefore, does not require antibodies. The capture of intact influenza viruses is of potential benefit for clinical diagnostics.
Translational control of inducible nitric oxide synthase expression by arginine can explain the arginine paradox (2003)

L-Arginine is the only endogenous nitrogen-containing substrate of NO synthase (NOS), and it thus governs the production of NO during nervous system development as well as in disease states such as stroke, multiple sclerosis, Parkinson's disease, and HIV dementia. The "arginine paradox" refers to the dependence of cellular NO production on exogenous L-arginine concentration despite the theoretical saturation of NOS enzymes with intracellular L-arginine. Herein, we report that decreased availability of L-arginine blocked induction of NO production in cytokine-stimulated astrocytes, owing to inhibition of inducible NOS (iNOS) protein expression. However, activity of the promoter of the iNOS gene, induction of iNOS mRNA, and stability of iNOS protein were not inhibited under these conditions. Our results indicate that inhibition of iNOS activity by arginine depletion in stimulated astrocyte cultures occurs via inhibition of translation of iNOS mRNA. After stimulation by cytokines, uptake of L-arginine negatively regulates the phosphorylation status of the eukaryotic initiation factor (eIF2 alpha), which, in turn, regulates translation of iNOS mRNA. eIF2 alpha phosphorylation correlates with phosphorylation of the mammalian homolog of yeast GCN2 eIF2 alpha kinase. As the kinase activity of GCN2 is activated by phosphorylation, these findings suggest that GCN2 activity represents a proximal step in the iNOS translational regulation by availability of l-arginine. These results provide an explanation for the arginine paradox for iNOS and define a distinct mechanism by which a substrate can regulate the activity of its associated enzyme.
Immunization with Recombinant Transferrin Binding Protein B Enhances Clearance of Nontypeable Haemophilus influenzae from the Rat Lung (1999)

ABSTRACT Nontypeable Haemophilus influenzae (NTHI) is an opportunistic pathogen, and heterogeneity in the surface-exposed immunodominant domains of NTHI proteins is thought to be associated with the failure of an infection to stimulate an immune response that is cross-protective against heterologous NTHI strains. The aim of this study was to assess the vaccine potential of a surface-exposed component of the NTHI human transferrin receptor, TbpB, and to determine if the antibody response elicited was cross-reactive with heterologous strains of NTHI. The efficacy of immunization with a recombinant form of TbpB (rTbpB) was determined by assessing the pulmonary clearance of viable bacteria 4 h after a live challenge with NTHI. There was a significant reduction in the number of viable bacteria in both the bronchoalveolar lavage fluid (34% for the 20-μg dose and 58% for the 40-μg dose) and lung homogenates (26% for the 20-μg dose and 60% for the 40-μg dose) of rats immunized with rTbpB compared to the control animals. While rTbpB-specific antibodies from immunized rats were nonspecific in the recognition of TbpB from six heterologous NTHI strains on Western blots, these antibodies differed in their ability to block transferrin binding to heterologous strains and to cross-react in bactericidal assays. If bactericidal antibodies are key indicators of the efficacy of the immune response in eliminating NTHI, this data suggests that while immunization with rTbpB stimulates protective responses against the homologous isolate, variability in the recognition of TbpB from heterologous isolates may limit the potential of rTbpB as an NTHI vaccine component.
Increased HIV-specific CD8+ T-cell cytotoxic potential in HIV elite controllers is associated with T-bet expression (2011)

Recent data suggest that CD8+ T-cell effector activity is an important component in the control of HIV replication in elite controllers (ECs). One critical element of CD8+ T-cell effector function and differentiation is the T-box transcription factor T-bet. In the present study, we assessed T-bet expression, together with the effector proteins perforin, granzyme A (Grz A), granzyme B (Grz B), and granulysin, in HIV-specific CD8+ T cells from ECs (n = 20), chronically infected progressors (CPs; n = 18), and highly active antiretroviral therapy (HAART)-suppressed individuals (n = 19). Compared with the other cohort groups, HIV-specific CD8+ T cells among ECs demonstrated a superior ability to express perforin and Grz B, but with no detectable difference in the levels of Grz A or granulysin. We also observed higher levels of T-bet in HIV-specific CD8+ T cells from ECs, with an ensuing positive correlation between T-bet and levels of both perforin and Grz B. Moreover, HIV-specific CD8+ T cells in ECs up-regulated T-bet to a greater extent than CPs after in vitro expansion, with concomitant up-regulation of perforin and Grz B. These results suggest that T-bet may play an important role in driving effector function, and its modulation may lead to enhanced effector activity against HIV.
Discovery of Cyclotides in the Fabaceae Plant Family Provides New Insights into the Cyclization, Evolution, and Distribution of Circular Proteins (2010)

Cyclotides are plant proteins whose defining structural features are a head-to-tail cyclized backbone and three interlocking disulfide bonds, which in combination are known as a cyclic cystine knot. This unique structural motif confers cyclotides with exceptional resistance to proteolysis. Their endogenous function is thought to be as plant defense agents, associated with their insecticidal and larval growth-inhibitory properties. However, in addition, an array of pharmaceutically relevant biological activities has been ascribed to cyclotides, including anti-HIV, anthelmintic, uterotonic, and antimicrobial effects. So far, >150 cyclotides have been elucidated from members of the Rubiaceae, Violaceae, and Cucurbitaceae plant families, but their wider distribution among other plant families remains unclear. Clitoria ternatea (Butterfly pea) is a member of plant family Fabaceae and through its usage in traditional medicine to aid childbirth bears similarity to Oldenlandia affinis, from which many cyclotides have been isolated. Using a combination of nanospray and matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) analyses, we examined seed extracts of C. ternatea and discovered cyclotides in the Fabaceae, the third-largest family of flowering plants. We characterized 12 novel cyclotides, thus expanding knowledge of cyclotide distribution and evolution within the plant kingdom. The discovery of cyclotides containing novel sequence motifs near the in planta cyclization site has provided new insights into cyclotide biosynthesis. In particular, MS analyses of the novel cyclotides from C. ternatea suggest that Asn to Asp variants at the cyclization site are more common than previously recognized. Moreover, this study provides impetus for the examination of other economically and agriculturally significant species within Fabaceae, now the largest plant family from which cyclotides have been described.
Enzymatic amplification of translation inhibition of rabbit β-globin mRNA mediated by anti-messenger oligodeoxynucleotides covalently linked to intercalating agents (1987)

The effects of anti-messenger oligodeoxynucleotides, covalently linked to an intercalating agent, on translation of rabbit beta-globin mRNA, were investigated both in wheat germ extract and in microinjected Xenopus oocytes. A specific inhibition of beta-globin synthesis was observed in both expression systems with a modified 11-mer covalently linked to an acridine derivative. In injected oocytes a more efficient block was observed with this modified oligonucleotide than with its unsubstituted homolog. This was ascribed to stacking interactions of the intercalating agent with base pairs which provide an additional stabilization of the [mRNA/DNA] hybrid. We demonstrated that in wheat germ extract, the modified and unmodified oligonucleotides behaved similarly due to the presence of a high RNaseH activity. RNaseH was also present, although to a lesser extent, in the oocyte cytoplasm. This anti-messenger DNA-induced degradation of target mRNA resulted in amplified efficiency of hybrid-arrested translation. This additional mechanism might provide anti-sense DNAs with an advantage over anti-sense RNAs.
Shotgun Proteomics and Biomarker Discovery (2002)

Coupling large-scale sequencing projects with the amino acid sequence information that can be gleaned from tandem mass spectrometry (MS/MS) has made it much easier to analyze complex mixtures of proteins. The limits of this "shotgun" approach, in which the protein mixture is proteolytically digested before separation, can be further expanded by separating the resulting mixture of peptides prior to MS/MS analysis. Both single dimensional high pressure liquid chromatography (LC) and multidimensional LC (LC/LC) can be directly interfaced with the mass spectrometer to allow for automated collection of tremendous quantities of data. While there is no single technique that addresses all proteomic challenges, the shotgun approaches, especially LC/LC-MS/MS-based techniques such as MudPIT (multidimensional protein identification technology), show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range. Advances in the ability to quantitate differences between samples and to detect for an array of post-translational modifications allow for the discovery of classes of protein biomarkers that were previously unassailable.
Mapping multiple independent synchronous dataflow graphs onto heterogeneous multiprocessors (2002)

We detail a method to facilitate development of real-time applications on heterogeneous multiprocessors. We introduce a new model of computation that allows for nondeterminate communication between independent dataflow graphs. The graphs may communicate in a manner that does not introduce data dependencies between them. We examine the implications of this model, introduce the necessary communication actors, and discuss scheduling techniques for multiple independent graphs. We also illustrate this model with some examples of real-time systems that have been constructed in Ptolemy.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The determination of the far field of an acoustic radiator from sparse measurement samples in the near field (1992)

The near-field to far-field projection procedure here introduced has the following novel features. (1) The measured near-field samples do not need to belong to a separable coordinate surface. (2) The number of samples is, in principle, as small as the theoretical number of degrees of freedom of the far field, related to the dimensions of the source in wavelengths. (3) The samples do not need to belong to a regular grid. (4) If the projection is sought only within a limited angular sector, a further reduction of the number of measurement samples is possible. The technique is based on the identification from the measured data of an equivalent monopolar distribution of acoustic sources on a surface completely surrounding the radiator. The far field of these sources, straightforwardly computed, constitutes the estimate of the far field of the radiator. The identification is based on the pseudo inversion of the matrix representing the mapping of the equivalent sources into near-field samples, which is obtained by resorting to the singular value decomposition of the matrix. Representative results of the extensive numerical simulations are here included.
Sub-micrometre accurate free-form optics by three-dimensional printing on single-mode fibres (2016)

Micro-optics are widely used in numerous applications, such as beam shaping, collimation, focusing and imaging. We use femtosecond 3D printing to manufacture free-form micro-optical elements. Our method gives sub-micrometre accuracy so that direct manufacturing even on single-mode fibres is possible. We demonstrate the potential of our method by writing different collimation optics, toric lenses, free-form surfaces with polynomials of up to 10th order for intensity beam shaping, as well as chiral photonic crystals for circular polarization filtering, all aligned onto the core of the single-mode fibres. We determine the accuracy of our optics by analysing the output patterns as well as interferometrically characterizing the surfaces. We find excellent agreement with numerical calculations. 3D printing of microoptics can achieve sufficient performance that will allow for rapid prototyping and production of beam-shaping and imaging devices.
Focal Volume Confinement by Submicrometer-Sized Fluidic Channels (2004)

Microfluidic channels with two lateral dimensions smaller than 1 microm were fabricated in fused silica for high-sensitivity single-molecule detection and fluorescence correlation spectroscopy. The effective observation volumes created by these channels are approximately 100 times smaller than observation volumes using conventional confocal optics and thus enable single-fluorophore detection at higher concentrations. Increased signal-to-noise ratios are also attained because the molecules are restricted to diffuse through the central regions of the excitation volume. Depending on the channel geometries, the effective dimensionality of diffusion is reduced, which is taken into account by simple solutions to diffusion models with boundaries. Driven by electrokinetic forces, analytes could be flowed rapidly through the observation volume, drastically increasing the rate of detection events and reducing data acquisition times. The statistical accuracy of single-molecule characterization is improved because all molecules are counted and contribute to the analysis. Velocities as high as 0.1 m/s were reached, corresponding to average molecular residence times in the observation volume as short as 10 micros. Applications of these nanofabricated devices for high-throughput, single-molecule detection in drug screening and genomic analysis are discussed.
Broad Wavelength Tunable Robust Lasing from Single-Crystal Nanowires of Cesium Lead Halide Perovskites (CsPbX3, X = Cl, Br, I) (2016)

Lead halide perovskite nanowires (NWs) are emerging as a class of inexpensive semiconductors with broad bandgap tunability for optoelectronics, such as tunable NW lasers. Despite exciting progress, the current organic-inorganic hybrid perovskite NW lasers suffer from limited tunable wavelength range and poor material stability. Herein, we report facile solution growth of single-crystal NWs of inorganic perovskite CsPbX3 (X = Br, Cl) and their alloys [CsPb(Br,Cl)3] and a low-temperature vapor-phase halide exchange method to convert CsPbBr3 NWs into perovskite phase CsPb(Br,I)3 alloys and metastable CsPbI3 with well-preserved perovskite crystal lattice and NW morphology. These single crystalline NWs with smooth end facets and subwavelength dimensions are ideal Fabry-Perot cavities for NW lasers. Optically pumped tunable lasing across the entire visible spectrum (420-710 nm) is demonstrated at room temperature from these NWs with low lasing thresholds and high-quality factors. Such highly efficient lasing similar to what can be achieved with organic-inorganic hybrid perovskites indicates that organic cation is not essential for light emission application from these lead halide perovskite materials. Furthermore, the CsPbBr3 NW lasers show stable lasing emission with no measurable degradation after at least 8 h or 7.2 × 10(9) laser shots under continuous illumination, which are substantially more robust than their organic-inorganic counterparts. The Cs-based perovskites offer a stable material platform for tunable NW lasers and other nanoscale optoelectronic devices.
Critical Review of Current Treatment Strategies for Advanced Hormone Insensitive Breast Cancer (2002)

Breast cancer is the most common cancer diagnosis in American women. Over the past several decades, there has been a steady increase in the incidence of this disease. Fortunately, the death rates in the last decade has showed a decrease. Patients with breast cancer now have more treatment options and a better chance of long term survival than ever before. Patients with metastatic disease are considered candidates for chemotherapy if they are symptomatic, have rapidly progressing or bulky disease, or if they are inappropriate candidates for hormonal therapy either because of negative hormonal receptor status or progression of disease on hormonal therapies. Patients are often treated with a chemotherapy regimen until progression of disease, or prohibitive toxicity, at which time the therapy is changed to a second or a third line therapy. This manuscript will provide a review of the current treatment strategies for advanced hormone insensitive breast cancer.
Photonic dispersion surfaces (1995)

Using the transfer matrix method for calculating the band structure, transmission and reflection coefficients of photonic systems, we present a method for calculating photonic dispersion surfaces. We then show how dispersion surfaces are excellent tools in the search for photonic insulators by applying the method to a simple system. We also explore the potential of metals for incorporation in photonic structures.