gebhart/patrepeval huggingface dataset:
Dynamic reconfiguration: Basic building blocks for autonomic computing on IBM pSeries servers (2003)

A Logical Partition (LPAR) in an IBM pSeries™ Symmetric Multiprocessor (SMP) system is a subset of the hardware of the SMP that can host an OS instance. Dynamic Reconfiguration (DR) on these logically partitioned servers enables the movement of hardware resources (such as processors, memory, and I/O slots) from one logical partition to another without requiring reboots. This capability also enables an autonomic agent to monitor usage of the partitions and automatically move hardware resources to a needy OS instance non-disruptively. Nowadays, as SMPs and NUMA systems get larger and larger, the ability to run several instances of an Operating System[s] on a given hardware system, so that each OS instance plus its subsystems scale or perform well, provides the advantage of optimal aggregate performance, which can translate to cost savings for the customers. Though static partitioning provides a solution to this overall performance optimization problem, DR enables an improved solution by providing the capability to dynamically move hardware resources to a needy OS instance in a timely fashion to match the workload demands. Hence DR capabilities serve as key building blocks for workload managers to provide self-opimizing and self-configuring features. Besides dynamic resource balancing, DR also enables dynamic capacity upgrade on demand, and self-healing features such as dynamic CPU sparing, a winning solution for users in this age of rapid growth in Web servers on the Internet.
Engineering the stability and the activity of a glycoside hydrolase (2010)

Glycosidases, the enzymes responsible in nature for the catabolism of carbohydrates, are well-studied catalysts widely used in industrial biotransformations and oligosaccharide synthesis, which are also attractive targets for drug development. Glycosidases from hyperthermophilic organisms (thriving at temperatures > 85 °C) are also interesting models to understand the molecular basis of protein stability and to produce robust tools for industrial applications. Here, we review the results obtained in the last two decades by our group on a β-glycosidase from the hyperthermophilic Archaeon Sulfolobus solfataricus. Our findings will be presented in the general context of the stability of proteins from hyperthermophiles and of the chemo-enzymatic synthesis of oligosaccharides.
The organization of taste sensibilities in hamster chorda tympani nerve fibers. (1988)

Electrophysiological measurements of nerve impulse frequencies were used to explore the organization of taste sensibilities in single fibers of the hamster chorda tympani nerve. Moderately intense taste solutions that are either very similar or easily discriminated were applied to the anterior lingual surface. 40 response profiles or 13 stimulus activation patterns were considered variables and examined with multivariate statistical techniques. Three kinds of response profiles were seen in fibers that varied in their overall sensitivity to taste solutions. One profile (S) showed selectivity for sweeteners, a second (N) showed selectivity for sodium salts, and a third (H) showed sensitivity to salts, acids, and other compounds. Hierarchical cluster analysis indicated that profiles fell into discrete classes. Responses to many pairs of effective stimuli were covariant across profiles within a class, but some acidic stimuli had more idiosyncratic effects. Factor analysis of profiles identified two common factors, accounting for 77% of the variance. A unipolar factor was identified with the N profile, and a bipolar factor was identified with the S profile and its opposite, the H profile. Three stimulus activation patterns were elicited by taste solutions that varied in intensity of effect. Hierarchical cluster analysis indicated that the patterns fell into discrete classes. Factor analysis of patterns identified three common unipolar factors accounting for 82% of the variance. Eight stimuli (MgSO4, NH4Cl, KCl, citric acid, acetic acid, urea, quinine HCl, HCl) selectively activated fibers with H profiles, three stimuli (fructose, Na saccharin, sucrose) selectively activated fibers with S profiles, and two stimuli (NaNO3, NaCl) activated fibers with N profiles more strongly than fibers with H profiles. Stimuli that evoke different patterns taste distinct to hamsters. Stimuli that evoke the same pattern taste more similar. It was concluded that the hundreds of peripheral taste neurons that innervate the anterior tongue play one of three functional roles, providing information about one of three features that are shared by different chemical solutions.
<i>Oldenlandia diffusa</i> and <i>Scutellaria barbata</i> Augment Macrophage Oxidative Burst and Inhibit Tumor Growth (1996)

Oldenlandia diffusa (OD) and Scutellaria barbata (SB) have been used in traditional Chinese medicine for treating liver, lung and rectal tumors. In this study we determined the effects of these phytochemicals on oxidative burst as an indicator of phagocytic function in a murine macrophage cell line J774 using an automated micro-fluorometric assay. A dose-dependent augmentation of oxidative burst was observed with OD as well as SB. The effect of OD and SB on the growth of a murine renal cell carcinoma (Renca) was also determined. Balb/c mice were transplanted subcutaneously with 1 x 10(5) Renca cells and were randomized into groups of 10 to receive oral feeding of OD (4 mg/day), SB (4 mg/day), or saline as control. Oral feeding with either OD or SB significantly inhibited the growth of Renca in mice. The data of this study show that OD and SB are capable of enhancing macrophage function in vitro and inhibiting tumor growth in vivo.
Engineering linear F(ab')<sub>2</sub> fragments for efficient production in <i>Escherichia coli</i> and enhanced antiproliferative activity (1995)

We developed a novel bivalent antibody fragment, the linear (L-) F(ab')2, comprising tandem repeats of a heavy chain fragment VH-CH1-VH-CH1 cosecreted with a light chain. Functional humanized L-F(ab')2 directed against p185HER2 was secreted from Escherichia coli at high titer (> or = 100 mg/l) and purified to homogeneity. The L-F(ab')2 binds two equivalents of antigen with an apparent affinity (Kd = 0.46 nM) that is within 3-fold of the corresponding thioether-linked F(ab')2 fragment. The N-terminal site binds antigen with an affinity (Kd = 1.2 nM) that is approximately 4-fold greater than that for the C-terminal site, as shown by the comparison of L-F(ab')2 variants containing a single functional binding site. L-F(ab')2 has greater antiproliferative activity than the thioether-linked F(ab')2 against the p185HER2-overexpressing tumor cell line BT474. Linear and thioether-linked F(ab')2 have very similar pharmacokinetic properties in normal mice, and their serum permanence times are respectively 7- and 8-fold longer than the corresponding Fab fragment. L-F(ab')2 offers a facile route to bivalent antibody fragments that are potentially suitable for clinical applications, and that may have improved biological activity compared with thioether-linked F(ab')2 fragments.
Intestinal response to growth factors administered alone or in combination with human [Gly<sup>2</sup>]glucagon-like peptide 2 (1997)

The control of intestinal epithelial growth is regulated by interactions of growth factors in various cellular compartments of the small and large bowel. Little information is available on the intestinal growth response to combinations of growth factors. We studied the intestinotrophic properties of a dipeptidyl peptidase IV resistant glucagon-like peptide 2 (GLP-2) analog, human [Gly2]GLP-2 (h[Gly2]GLP-2), as well as of epidermal growth factor (EGF), long [Arg3]insulin-like growth factor I (LR3IGF-I), [Gly1]IGF-II, and human growth hormone (hGH), administered by subcutaneous injection alone or in combination in mice. At the doses tested, h[Gly2]GLP-2 was the most potent agent for increasing small and large bowel mass. Mice treated with h[Gly2]GLP-2 and either GH or IGF-I exhibited greater increases in histological parameters of small intestinal growth than did mice treated with h[Gly2]GLP-2 alone. Administration of all five growth factors together induced significant increases in crypt plus villus height and in small and large bowel length and weight. The results of these experiments define regional differences in both the cellular targets and relative activities of intestinotrophic molecules and raise the possibility that selective growth factor combinations may be useful for enhancement of intestinal adaptation in vivo.
Binding-Pocket and Lid-Region Substitutions Render Human STING Sensitive to the Species-Specific Drug DMXAA (2014)

The drug DMXAA (5,6-dimethylxanthenone-4-acetic acid) showed therapeutic promise against solid tumors in mouse models but subsequently failed in human clinical trials. DMXAA was later discovered to activate mouse, but not human, STING, an adaptor protein in the cyclic dinucleotide cGAMP-mediated signaling pathway, inducing type I interferon expression. To facilitate the development of compounds that target human STING, we combined structural, biophysical, and cellular assays to study mouse and human chimeric proteins and their interaction with DMXAA. We identified a single substitution (G230I) that enables a DMXAA-induced conformational transition of hSTING from an inactive "open" to an active "closed" state. We also identified a substitution within the binding pocket (Q266I) that cooperates with G230I and the previously identified S162A binding-pocket point substitution, rendering hSTING highly sensitive to DMXAA. These findings should facilitate the reciprocal engineering of DMXAA analogs that bind and stimulate wild-type hSTING and their exploitation for vaccine-adjuvant and anticancer drug development.
Evaluation of an on-line adaptive gesture interface with command prediction (2005)

We present an evaluation of a hybrid gesture interface framework that combines on-line adaptive gesture recognition with a command predictor. Machine learning techniques enable on-line adaptation to differences in users' input patterns when making gestures, and exploit regularities in command sequences to improve recognition performance. A prototype using 2D single-stroke gestures was implemented with a minimally intrusive user interface for on-line re-training. Results of a controlled user experiment show that the hybrid adaptive system significantly improved overall gesture recognition performance, and reduced users' need to practice making the gestures before achieving good results.
Stored waveform inverse Fourier transform axial excitation/ejection for quadrupole ion trap mass spectrometry (1993)

A general method for high-resolution ion excitation, ejection, and isolation is developed from linear response theory for resonant dipolar excitation of the axial z-oscillatory motion of ions in a quadrupole (Paul) ion trap operated in rf-only mode. For a spatially uniform dipolar excitation field, the ion z-oscillation amplitude is directly proportional to the amplitude of the Fourier component of the excitation at the axial oscillation frequency of that ion. Thus, one may specify an arbitrary z-motion frequency-domain spectrum by applying a time-domain stored waveform obtained from the inverse Fourier transform of the corresponding frequency-domain excitation spectrum. The stored waveform inverse Fourier transform (SWIFT) waveform may be tailored for selective ejection or excitation of ions of arbitrary mass-to-charge ratio ranges. The method includes all other possible excitation/ejection waveforms (e.g., single frequency, frequency sweep) as special cases. The effect of collisional damping during excitation is included in the analytical solution of the ion response.
Phage-display evolution of tyrosine kinases with altered nucleotide specificity (2001)

The problem of identifying downstream targets of kinase phosphorylation remains a challenge despite technological advances in genomics and proteomics. A recent approach involves the generation of kinase mutants that can uniquely use "orthogonal" ATP analogs to phosphorylate substrates in vivo. Using structure-based design, mutants of several protein kinase superfamily members have been found; robust and general methods are needed, however, for altering the nucleotide specificity of the remaining kinases in the genome. Here we demonstrate the application of a new phage display technique for direct functional selection to the identification of a tyrosine kinase mutant with the ability to use N6-benzyl-ATP. Our method produces, in five rounds of selection, a mutant identical to the best orthogonal Src kinase found to date. In addition, we isolate from a larger library of kinase mutants a promiscuous clone capable of using many different ATP analogs. This approach to engineering orthogonal kinases, combined with others, will facilitate the mapping of phosphorylation targets of any kinase in the genome.
Effects of hepatocyte growth factor on the growth and metabolism of human hepatocytes in primary culture (1995)

The effect of recombinant human hepatocyte growth factor (h-rHGF), a potent mitogen for hepatocytes, was investigated in primary cultures of human hepatocytes. Here, we describe a series of experiments to investigate the kinetics of its mitogenic action, as well as its metabolic effects on cultured human hepatocytes. The h-rHGF is a potent signal for initiating DNA synthesis in human hepatocytes, with maximal stimulatory effects at 10 ng/mL (0.1 pmol/L). The kinetics of DNA synthesis showed a lag of about 48 to 72 hours, followed by a maximum at 96 hours. At least 48 hours of continuous exposure to h-rHGF are required to initiate DNA synthesis in quiescent human hepatocytes. Cell cycle analysis by flow cytometry showed that most of quiescent 2c cells have left G0/G1 and entered the cell cycle (S and G2/M phases) by 96 hours of continuous exposure to h-rHGF. When compared with other growth factors, h-rHGF was a much more potent mitogen. The effects of 10 ng/mL (0.1 pmol/L) h-rHGF on DNA synthesis were only achieved by 1.5 pmol/L epidermal growth factor (EGF), 0.1 mumol/L insulin, or 1 mumol/L glucagon. It is noteworthy that the effect of h-rHGF was potentiated by glucagon but not by insulin or EGF. The stimulatory effect of HGF on DNA synthesis was gradually inhibited by h-rHGF transforming growth factor beta (TGF-beta) in the range 1 to 10 ng/ml. The HGF also influenced the expression of other hepatic genes.(ABSTRACT TRUNCATED AT 250 WORDS)
Simultaneous and Extensive Site-specific N- and O-Glycosylation Analysis in Protein Mixtures (2011)

Extensive site-specific glycosylation analysis of individual glycoproteins is difficult due to the nature and complexity of glycosylation in proteins. In protein mixtures, these analyses are even more difficult. We present an approach combining nonspecific protease digestion, nanoflow liquid chromatography, and tandem mass spectrometry (MS/MS) aimed at comprehensive site-specific glycosylation analysis in protein mixtures. The strategy described herein involves the analysis of a complex mixture of glycopeptides generated from immobilized-Pronase digestion of a cocktail of glycoproteins consisting of bovine lactoferrin, kappa casein, and bovine fetuin using nanoflow liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (nano-LC-Q-TOF MS). The resulting glycopeptides were chromatographically separated on a micro fluidic chip packed with porous graphitized carbon and analyzed via MS and MS/MS analyses. In all, 233 glycopeptides (identified based on composition and including isomers) corresponding to 18 glycosites were observed and determined in a single mixture. The glycopeptides were a mixture of N-linked glycopeptides (containing high mannose, complex and hybrid glycans) and O-linked glycopeptides (mostly sialylated). Results from this study were comprehensive as detailed glycan microheterogeneity information was obtained. This approach presents a platform to simultaneously characterize N- and O-glycosites in the same mixture with extensive site heterogeneity.
Simultaneous block and I/O buffer floorplanning for flip-chip design (2006)

The flip-chip package gives the highest chip density of any packaging method to support the pad-limited ASIC design. One of the most important characteristics of flip-chip designs is that the input/output buffers could be placed anywhere inside a chip. In this paper, we first introduce the floorplanning problem for the flip-chip design and formulate it as assigning the positions of input/output buffers and first-stage/last-stage blocks so that the path length between blocks and bump balls as well as the delay skew of the paths are simultaneously minimized. We then present a hierarchical method to solve the problem. We first cluster a block and its corresponding buffers to reduce the problem size. Then, we go into iterations of the alternating and interacting global optimization step and the partitioning step. The global optimization step places blocks based on simulated annealing using the B*-tree representation to minimize a given cost function. The partitioning step dissects the chip into two subregions, and the blocks are divided into two groups and are placed in respective subregions. The two steps repeat until each subregion contains at most a given number of blocks, defined by the ratio of the total block area to the chip area. At last, we refine the floorplan by perturbing blocks inside a subregion as well as in different subregions. Compared with the B*-tree based floorplanner alone, our method is more efficient and obtains significantly better results, with an average cost of only 51.8% of that obtained by using the B*-tree alone, based on a set of real industrial flip-chip designs provided by leading companies.
The use of fluorescence detection and internal lane standards to size PCR products automatically. (1992)

We have developed chemical procedures, optical and electrophoretic instrumentation and computer software automate the analysis of polymerase chain reaction (PCR) products. DNA molecules labeled with up to four different fluorescent dyes are analyzed within a single electrophoresis gel lane. A size calibration curve is created for each electrophoresis lane from the electrophoretogram of uniquely labeled DNA fragments belonging to an internal lane standard that co-electrophoreses with the PCR products. The unknown molecular lengths of PCR products are automatically calculated from the calibration curve. Data from control experiments with DNA segments of known molecular length demonstrate the accuracy and precision of such sizing. This system has been applied to the analysis of PCR products for research in the areas of human identification, genetic mapping and genetic disease.
Oxidative Burst in Alfalfa-<i>Sinorhizobium meliloti</i> Symbiotic Interaction (2001)

Reactive oxygen species are produced as an early event in plant defense response against avirulent pathogens. We show here that alfalfa responds to infection with Sinorhizobium meliloti by production of superoxide and hydrogen peroxide. This similarity in the early response to infection by pathogenic and symbiotic bacteria addresses the question of which mechanism rhizobia use to counteract the plant defense response.
Increased Fecal Bile Acid Excretion in Transgenic Mice With Elevated Expression of Human Phospholipid Transfer Protein (2003)

Our data show that elevation of PLTP activity results in rapid disposal of cholesterol from the body via increased conversion into bile acids and subsequent excretion.
A high-efficiency CMOS voltage doubler (1998)

A charge pump cell is used to make a voltage doubler using improved serial switches. A complete power efficiency theory is presented which fits the measurements. The importance of capacitors is shown with plots of power efficiency versus load and stray capacitors. Several problems arising at low voltage or high frequency are developed and some optimizations are presented. The substrate current is totally suppressed by the technique of bulk commutation. A power efficiency of 95% has been reached using external capacitors. A fully integrated charge pump is also presented and shows a maximum power efficiency of 75%.
Low Force Shear Rams: The Future is More (2011)

Abstract With the increased usage of stronger and tougher tubulars in today's well construction, the ability to shear in the blowout preventor (BOP) without turning to larger operators is an economic necessity. Existing rigs need ways to drill with the high performance steelavailable today without having to grow the size of the BOP. This paper will discuss the mechanics of shear and how it applies to V Shear technology of yesterday as well as the current Low Force Shear of today and tomorrow. The Low Force Shear technology provides the technology to extend the capabilities of present day BOPs through major improvements in shear ram design. These shears substantially reduce the forces needed to cut tubulars. Lower forces mean that both stronger and larger diameter tubulars can be managed with the same shear operators, adding value to the existing stack and saving the contractor a major outlay for increased BOP capabilities and corresponding handling equipment upgrades. Low Force Shear technology is based in the philosophy of final shear area reduction. Getting more of the cross sectional area cut prior to the final shear reduces the forces required in that final shear by leaving a smaller remainder cross sectional area to be cut. By puncturing the tubular first and managing the design of the sheared material (chip management), the Low Force Shear begins effectively cutting material earlier and farther before reaching the final shear section. As the development of the Low Force Shear is optimized for various diameters, material properties, and cross sectional areas, the opportunities expand to increase the range and variety of items in the well bore that can be cut that were not previously thought possible. This capability would greatly increase the security of the well. The future frontier is "Shearing More".
Sera and conditioned media contain different isoforms of platelet-derived growth factor (PDGF) which bind to different classes of PDGF receptor (1989)

Platelet-derived growth factor (PDGF) is encoded by separate genes for two possible subunit chains (A-chain and B-chain) which can form three possible dimers (AA, AB, and BB). We have recently presented evidence that multiple forms of PDGF receptor exist which distinguish between these isoforms (Hart, C. H., Forstrom, J. W., Kelley, J. D., Smith, R. A., Ross, R., Murray, M. J., and Bowen-Pope, D. F. (1988) Science 240, 1529-1531). We used this specificity to determine the amount of PDGF from different sources which is able to bind to each class of receptor and found that each source had a characteristic isoform composition. Levels of total PDGF activity in sera from different species ranged more than 15-fold, from less than 1 ng/ml in dog, chicken, pig, and calf, to greater than 13 ng/ml in mouse and human. Despite these differences in PDGF content, the total mitogenic activities of the sera were comparable indicating that the relative importance of PDGF as a serum mitogen may vary considerably between species. Analysis of the total PDGF into the amounts of each isoform revealed great differences in composition. PDGF-BB constitutes only about 15% of the total binding activity in human PDGF purified by the method of Raines and Ross (Raines, E. W., and Ross, R. (1982) J. Biol. Chem. 257, 5154-5160) but is the predominant isoform in whole blood serum from all other species. In contrast to serum, medium conditioned by cultured PDGF-secreting cell types contained no detectable PDGF-BB except in two cases: medium conditioned by vascular endothelial cells and by cells transformed by simian sarcoma virus. The existence of isoform-specific PDGF receptors and the large variation in PDGF isoform composition dependent upon source may provide an important mechanism through which the effects of PDGF can be targeted to different cell types and/or toward eliciting different cell responses.