gebhart/patrepeval huggingface dataset:
AUTOMATED LAYOUT-INCLUSIVE SYNTHESIS OF ANALOG CIRCUITS USING SYMBOLIC PERFORMANCE MODELS (2005)

A key task in the automated design of analog/RF circuits is circuit sizing, a process that involves assigning numerical values to unknown circuit parameters of a fixed topology, while being subjected to a set of performance constraints.Over the years, the terms sizing and synthesis have been used interchangeably, and have become synonymous in the analog domain.Mature tools for the synthesis of digital circuits are abundant, but the market for analog synthesis tools is still growing and very few commercial products exist.Several techniques have been developed in the past for analog synthesis, ranging from knowledge-based methods to techniques using numerical simulation.A frequently used technique involves an iterative stochastic search, which uses numerical simulations at every probable design point, in order to obtain the performance metrics.Expensive computations and parasitics unawareness of this traditional method necessitates a scheme which can produce fast layout aware designs.In this dissertation a new synthesis methodology, which uses parameterized layout generators and symbolic performance models (SPMs) inside the synthesis loop, has been developed to overcome the deficiencies of the previous circuit sizing method.This layout-inclusive (layoutin-loop) approach uses efficient parameterized procedural layout generators, obtained using Leuven, Belgium, for their permission to use the DDKUL software.Their guidance also has been very important in my research.I thank Dr. Andrea Pacelli for the VPEC software suite.I also thank my colleagues Anuradha
Quantitative Chemical Proteomics for Identifying Candidate Drug Targets (2003)

We have developed a systematic strategy for drug target identification. This consists of the following sequential steps: (1) enrichment of total binding proteins using two differential affinity matrixes upon which are immobilized positive and negative chemical structures for drug activity, respectively; (2) covalent labeling of the proteins with a new cleavable isotope-coded affinity tag (ICAT) reagent, followed by proteolysis of the combined proteins; (3) isolation, identification, and relative quantification of the tagged peptides by liquid chromatography-mass spectrometry; (4) array-based transcription profiling to select candidate proteins; and (5) confirmation of direct interaction between the activity-associated structure and the selected proteins by using surface plasmon resonance. We present a typical application to identify the primary binding protein of a novel class of anticancer agents exemplified by E7070. Our results suggest that this approach provides a new aspect of quantitative proteomics to find specific binding proteins from protein mixture and should be applicable to a wide variety of biologically active small molecules with unidentified target proteins.
RETRACTED: Adaptive Amphiphilic Dendrimer‐Based Nanoassemblies as Robust and Versatile siRNA Delivery Systems (2014)

siRNA delivery remains a major challenge in RNAi-based therapy. Here, we report for the first time that an amphiphilic dendrimer is able to self-assemble into adaptive supramolecular assemblies upon interaction with siRNA, and effectively delivers siRNAs to various cell lines, including human primary and stem cells, thereby outperforming the currently available nonviral vectors. In addition, this amphiphilic dendrimer is able to harness the advantageous features of both polymer and lipid vectors and hence promotes effective siRNA delivery. Our study demonstrates for the first time that dendrimer-based adaptive supramolecular assemblies represent novel and versatile means for functional siRNA delivery, heralding a new age of dendrimer-based self-assembled drug delivery in biomedical applications.
Fabrication and Biocompatibility of Carbon Nanotube-Based 3D Networks as Scaffolds for Cell Seeding and Growth (2004)

Thin film networks of multiwalled carbon nanotubes (MWCNTs) were prepared by exerting chemically induced capillary forces upon the nanotubes. During this process MWCNTs undergo a transformation from being a vertically aligned structure to an interlocking resistive network of interconnected nanotubes, whose main feature is a regular three-dimensional (3D) sieve architecture. Due to their structural characteristics at the nanoscale level, 3D-MWCNT-based networks are in principle ideal candidates for scaffolds/matrices in tissue engineering. Their potential application in this field was confirmed by extensive growth, spreading, and adhesion of the common mouse fibroblast cell line L929.
Space-time codes for wireless communication (2002)

The design of channel codes for improving the data rate and/or the reliability of communications over fading channels using multiple transmit antennas is considered. A design criterion is provided and is then used to design space-time codes for high data rate wireless communication. These codes are trellis codes that are easy to encode and decode and have remarkable performance.
Na+/H+ Exchangers of Mammalian Cells (1997)

Ejection of intracellular H+ in exchange for external Na+ is the most effective means of eliminating excess acid from actively metabolizing cells. Na+/H+ exchange is also crucial for the regulation of the cellular volume and for the reabsorption of NaCl across renal, intestinal, and other epithelia. This remarkable array of essential functions is carried out by a family of antiporters, known generically as Na+/H+ exchangers (NHEs).1 These are highly regulated (glyco)phosphoproteins present in virtually all mammalian tissues and species studied to date.
Power efficient 4.5Gbit/s optical receiver in 130nm CMOS with integrated photodiode (2008)

An optical receiver with integrated photodiode in 130 nm CMOS is presented. The extremely unfavourable optical and electrical performance of a differential photodiode in this technology, namely a very low responsivity of only 5 mA/W, an optical bandwidth of 500 MHz and a large photodiode capacitance of 1pF, have been solved so that bitrates of 4.5Gbit/s and higher can be received for BER values as low as 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-12</sup> . The power consumption for this is only 74.16 mW due to a biasing in weak inversion.
Strain-based Genetic Differences Regulate the Efficiency of Systemic Gene Delivery as Well as Expression (2002)

We have characterized the impact of strain-based genetic differences on the efficiency of the intravenous cationic liposome-DNA complex (CLDC)-based gene transfer and expression in mice. We also investigated what steps in the gene delivery and expression pathway appeared responsible for these strain-related differences and whether such differences could be compensated for either by agents that alter host pathways important in CLDC-mediated gene transfer and expression, or by changes in CLDC formulation. We found that different mouse strains can exhibit different expression levels and/or differences in the amount of plasmid DNA delivered to the organs where the DNA is expressed. Furthermore, drug pretreatment or reformulation of the CLDC could improve DNA delivery and/or gene expression in a strain-specific fashion. We conclude that genetic factors critically modify both the tissue deposition and the expression of genetic materials delivered by CLDC. Because manipulation of either the host or the CLDC could at least partially compensate for these strain-related differences, such strategies may be required to effectively use non-viral gene transfer approaches in genetically diverse populations.
Creativity support tools: accelerating discovery and innovation (2007)

How can designers of programming interfaces, interactive tools, and rich social environments enable more people to be more creative more often?
Chenodeoxycholate Is an Inhibitor of Clostridium difficile Spore Germination (2008)

Some cholate derivatives that are normal components of bile can act with glycine to induce the germination of Clostridium difficile spores, but at least one bile component, chenodeoxycholate, does not induce germination. Here we show that chenodeoxycholate inhibits the germination of C. difficile spores in response to cholate and taurocholate.
The Antifungal Drug Itraconazole Inhibits Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) Glycosylation, Trafficking, and Signaling in Endothelial Cells (2011)

Background: Itraconazole is a widely used antifungal drug that was recently found to possess potent antiangiogenic activity. Results: We report here that itraconazole caused accumulation of immature N-glycans on VEGFR2 and inhibited VEGFR2 trafficking and signaling. Conclusion: These results suggest that itraconazole interferes with VEGFR2 trafficking, glycosylation, and signaling activity. Significance: Itraconazole possesses unique antiangiogenic potential through targeting multiple pathways that are essential for angiogenesis.
Polyhydroxyalkanoic acids (1991)

Polyhydroxyalkanoic acids (PHA) are water-insoluble polyesters of alkanoic acids containing a hydroxyl group as at least one functional group in addition to the carboxy group, and possess the general formula shown in Fig. 1. Although some of these polymers are also available from chemical synthesis, many of them are synthesized by bacteria and are deposited in abundant amounts in the cytoplasm of the cells. The variability of the position of the hydroxyl group and of the type of the R-pendant group of the constituents (see below), a large variety of different constituent monomers in copolyesters, as well as the varying degree of polymerization, allow the biosynthesis of many different polymers exhibiting different physical properties.
Coagulation Factor VII Mass and Activity in Young Men With Myocardial Infarction at a Young Age (1995)

Factor VII (FVII) coagulant activity has been proven to be associated with the risk of future fatal coronary heart disease (CHD) in middle-aged men. Recent studies have emphasized the role of triglyceride-rich lipoproteins and FVII genotype in determining plasma levels of FVII protein and activity. The present study was undertaken to examine whether FVII activity state and protein concentration in fasting plasma are altered in young men with proven myocardial infarction (MI) and examined the relations of FVII to subfractions of apo B-containing lipoproteins and the Arg-->Gln polymorphism in the FVII gene. Activated FVII (FVIIa) was determined by a clotting assay using soluble, recombinant, truncated tissue factor. A total of 94 men with a first MI before the age of 45 (mean age +/- SD, 39.6 +/- 4.5 years) were included in the study along with 99 population-based, age-matched control subjects. In addition to FVIIa and FVII antigen (FVII:Ag), a panel of FVII activity assays were included for comparison with previous work in this field. The plasma level of FVII:Ag was higher in patients than in control subjects when the entire groups were compared (537 +/- 128 versus 479 +/- 93 ng/mL, P < .001), the differences being accounted for by patients with hypertriglyceridemic lipoprotein phenotypes. In contrast, FVIIa was similar in patients and control subjects (4.6 +/- 1.4 versus 4.3 +/- 1.3 ng/mL, NS), which means that the proportion of FVIIa molecules was unaltered or even lower in the patients. As expected, the Arg-->Gln polymorphism significantly influenced both FVII mass and activity levels. In addition, presence of the Gln allele appeared to be associated with a lower proportion of fully active FVII molecules. The polymorphism also affected the relation between the plasma concentration of VLDL and FVII:Ag. The triglyceride content and particle number of all VLDL subfractions, irrespective of particle size, correlated fairly strongly with FVII mass determinations but not at all with FVIIa. HDL cholesterol concentration, on the other hand, presumably reflecting the efficiency of lipoprotein lipase-mediated lipolysis of VLDL, related significantly to the FVIIa level. The Arg-->Gln polymorphism, independent of lipoprotein effects, explained 5% to 10% of the variation in FVII mass and activity. In conclusion, the present findings speak against a role of FVII as a risk factor for CHD, because a significantly increased potential for activation of coagulation (ie, raised basal concentration of FVIIa) was not observed among young postinfarction patients.(ABSTRACT TRUNCATED AT 400 WORDS)
Potentiation of Nerve Growth Factor-Induced Neurite Outgrowth in PC12 Cells by Ifenprodil: The Role of Sigma-1 and IP3 Receptors (2012)

In addition to both the α1 adrenergic receptor and N-methyl-D-aspartate (NMDA) receptor antagonists, ifenprodil binds to the sigma receptor subtypes 1 and 2. In this study, we examined the effects of ifenprodil on nerve growth factor (NGF)-induced neurite outgrowth in PC12 cells. Ifenprodil significantly potentiated NGF-induced neurite outgrowth, in a concentration-dependent manner. In contrast, the α1 adrenergic receptor antagonist, prazosin and the NMDA receptor NR2B antagonist, Ro 25-6981 did not alter NGF-induced neurite outgrowth. Potentiation of NGF-induced neurite outgrowth mediated by ifenprodil was significantly antagonized by co-administration of the selective sigma-1 receptor antagonist, NE-100, but not the sigma-2 receptor antagonist, SM-21. Similarly, ifenprodil enhanced NGF-induced neurite outgrowth was again significantly reduced by the inositol 1,4,5-triphosphate (IP(3)) receptor antagonists, xestospongin C and 2-aminoethoxydiphenyl borate (2-APB) treatment. Furthermore, BAPTA-AM, a chelator of intracellular Ca(2+), blocked the effects of ifenprodil on NGF-induced neurite outgrowth, indicating the role of intracellular Ca(2+) in the neurite outgrowth. These findings suggest that activation at sigma-1 receptors and subsequent interaction with IP(3) receptors may mediate the pharmacological effects of ifenprodil on neurite outgrowth.
Polarization self-modulation of the nonstationary speckle field in a photorefractive crystal (1999)

We have observed the nonstationary polarization modulation of a speckle pattern transmitted through a photorefractive crystal under the alternating electric field of a square-wave form. A simple model based on Gaussian-beam propagation in the crystal with the diffusion type of nonlinearity is proposed to explain the main features of the experiment. Application of the phenomenon to noncontact and highly sensitive measurements of a rough surface movement is suggested.
Optical Analysis of Synaptic Vesicle Recycling at the Frog Neuromuscular Junction (1992)

The fluorescent dyes FM1-43 and RH414 label motor nerve terminals in an activity-dependent fashion that involves dye uptake by synaptic vesicles that are recycling. This allows optical monitoring of vesicle recycling in living nerve terminals to determine how recycled vesicles reenter the vesicle pool. The results suggest that recycled vesicles mix with the pool morphologically and functionally. One complete cycle of release of transmitter, recycling of a vesicle, and rerelease of transmitter appears to take about 1 minute.
Are small changes in serum creatinine an important risk factor? (2005)

Acute elevations in serum creatinine had a linear association with increased risk for adverse outcomes among patients hospitalized for cardiac surgery or heart failure. Future studies should determine interventions to prevent and treat in-hospital worsening renal function to reduce the risk for adverse outcomes.
Evaluating a brief prevention program for improving marital conflict in community families. (2008)

Marital conflict is related to well-being in children and adults (E. M. Cummings & P. T. Davies, 2002). Marital conflict is likely most effectively ameliorated before it becomes clinically significant. However, families without significant problems may be unwilling to participate in couples therapies or other lengthy or intensive interventions. Responding to this gap, the authors developed a 4-session psychoeducational program about marital conflict for community families. Couples with children 4-8 years of age were randomly blocked into 1 of 3 groups: (1) a parent-only group (n = 24), (2) a parent-child group (n = 33), or (3) a self-study group (n = 33). Pre- and posttest and 6-month and 1-year assessments were conducted. This report evaluates (a) whether participation in a psychoeducational program for parents improved marital conflict, especially concerning ways of expressing disagreements, and (b) whether changes in marital conflict subsequently improved marital satisfaction, parenting, and child adjustment. Greater constructive and less destructive marital conflict was observed at all assessments for treatment groups, and these changes were linked with improvements in other family processes. The findings support the promise of brief, psychoeducational programs for improving marital conflict for community samples.
INVIVOMEASUREMENT OFFLUXES THROUGHMETABOLICPATHWAYS: The Missing Link in Functional Genomics and Pharmaceutical Research (2003)

In the postgenomic era of biology, much attention has been given to functional genomics, or the relation between genes and higher levels of organization in the cell. The latter are typically represented as mRNA, protein, or organic metabolite complements. The theme of this review is that the operational unit of function in complex biological systems is more properly seen as the fully assembled metabolic pathway in the whole organism. Due to the connectivity, interactions, and complexity of metabolic pathways, the measurement of components is an inadequate method for predicting phenotype. Measurement of the outputs of pathways (molecular fluxes) involves different tools than static measures of components, however. Here, we review recently developed stable isotope-mass spectrometric tools for measuring fluxes through metabolic pathways in vivo, focusing on the response to dietary macronutrients (carbohydrates and fats). Methods discussed include measurement of lipid dynamics, DNA replication, hepatic assembly of lipoproteins, and long-lived protein synthesis. Measuring fluxes through multiple pathways concurrently allows regulatory themes to emerge. Use of 2H2O-labeling is emerging as a particularly powerful approach for multiple concurrent biosynthetic flux measurements. Several examples demonstrate that pathway flux results are often unexpected and not predicted by classic biochemistry or the expression of genes and proteins.
Conjoining specifications (1995)

We show how to specify components of concurrent systems. The specification of a system is the conjunction of its components' specifications. Properties of the system are proved by reasoning about its components. We consider both the decomposition of a given system into parts, and the composition of given parts to form a system.
Rapid Radioimmunoassay Diagnosis of Legionnaires' Disease (1981)

Urine from nine patients with serogroup 1 Legionnaires' disease, 100 with infected or contaminated urine, 50 with bacteremic infections, 26 with infectious or infiltrative pulmonary diseases, and 65 with miscellaneous infectious or noninfectious illnesses, was examined by radioimmunoassay for the presence of Legionella pneumophila antigen(s). Urine of all nine Legionnaires' disease patients was clearly differentiated from that of the 241 control subjects by the assay. The antigen was detected from 2 to at least 10 days after the initiation of erythromycin therapy. A probable false-positive results occurred in a patient with necrotizing nosocomial pneumonia who died before definitive serologic evaluation for Legionnaires' disease could be completed. The antigen was stable at 100 degrees C for 30 minutes and was not degraded by trypsin. Its elution behavior suggested that its molecular weight is approximately 10 000. The radioimmunoassay appears to be a useful method for rapidly diagnosing serogroup 1 Legionnaires' disease.
A Bead‐Based Proximity Assay for BRD4 Ligand Discovery (2015)

Bromodomain-containing proteins have emerged as desirable targets for anti-neoplastic and anti-inflammatory drug discovery. Toward the development of selective inhibitors of the BET family of bromodomains, we optimized bead-based assays to detect interactions between bromodomains and poly-acetylated histone peptides. Donor and acceptor beads bound to target and ligand are brought into proximity by this protein-protein interaction. After laser illumination, singlet oxygen evolved from donor beads travels to the spatially close acceptor beads, resulting in chemiluminesence. This AlphaScreen assay has proven amendable to high-throughput screening, secondary validation, and specificity profiling during lead discovery and optimization. Here we report our protocol for assay development to measure inhibition of ligand binding to bromodomain-containing protein 4 (BRD4). We discuss the discovery of an appropriate probe, optimization of bead, probe, and protein concentrations, and the derivation of protein-probe inhibition curves. Finally, we explore the implementation of this technology for high-throughput screening of potential BRD4 inhibitors.
Sybase SQL Server 11 Unleashed (1996)

From the Publisher:
Programmers will want the most comprehensive, day-and-date material on the new release of Sybase System 11. Sybase SQL Server 11 Unleashed addresses that need by providing information on all important programming and database administration topics relevant to the new release.
Teaches how to manage the new features of System 11
CD-ROM includes the source code from the book, Aurora Desktop, a compact SQL Editor, and a full-size Aurora Script Manager
Argonaute Journeys into the Heart of RISC (2004)

Identifying the component of the RNA-induced silencing complex (RISC) complex has been a major goal of those interested in the RNA interference pathway of gene silencing. In their Perspective, [Sontheimer and Carthew][1] discuss a pair of recent studies ([ Liu et al .][2], [ Song et al .][3]) that identify the protein Argonaute2 as the slicer element of RISC that cleaves target messenger RNAs.

 [1]: http://www.sciencemag.org/cgi/content/full/305/5689/1409
 [2]: http://www.sciencemag.org/cgi/content/short/305/5689/1437
 [3]: http://www.sciencemag.org/cgi/content/short/305/5689/1434
SINGLE CELL DEGENERATE OLIGONUCLEOTIDE PRIMER-PCR AND COMPARATIVE GENOMIC HYBRIDIZATION WITH MODIFIED CONTROL REFERENCE (2001)

For investigating the possibility of applying degenerate oligonucleotide primer PCR (DOP-PCR) and comparative genomic hybridization (CGH) technique to analyses of genomic genetics in a single cell, the whole genomic DNA of a single cell with XX, XY, XO, XXY, +13 or +21 was amplified by DOP-PCR. Single cell DOP-PCR CGHs with conventional and modified control references, the genomic DNA and a single cell DOP-PCR product from normal male, were carried out respectively. The results showed that the average profile of the fluorescence intensity ratio in CGH with the genomic DNA as reference fluctuates much and that the standard deviation in about 30% haploid is beyond the normal limits. False positive hyper-representation was found to exist in X chromosome while trisomy 13 and 21 were not detected. However, the distributions of the mean and the standard deviation of the ratio in the CGH with DOP-PCR product as reference were quite acceptable. The copy number changes of chromosome X, Y, 13 and 21 were revealed. Those results suggested that there is unrandom unequal amplification in a single cell DOP-PCR. Using a single DOP-PCR product as reference can decrease its influence on CGH. Single cell DOP-PCR-CGH and its application in the genetic analyses of preimplantation embryo or fetal cell in maternal blood may be possible.