gebhart/patrepeval huggingface dataset:
Efficient coflow scheduling with Varys (2014)

Communication in data-parallel applications often involves a collection of parallel flows. Traditional techniques to optimize flow-level metrics do not perform well in optimizing such collections, because the network is largely agnostic to application-level requirements. The recently proposed coflow abstraction bridges this gap and creates new opportunities for network scheduling. In this paper, we address inter-coflow scheduling for two different objectives: decreasing communication time of data-intensive jobs and guaranteeing predictable communication time. We introduce the concurrent open shop scheduling with coupled resources problem, analyze its complexity, and propose effective heuristics to optimize either objective. We present Varys, a system that enables data-intensive frameworks to use coflows and the proposed algorithms while maintaining high network utilization and guaranteeing starvation freedom. EC2 deployments and trace-driven simulations show that communication stages complete up to 3.16X faster on average and up to 2X more coflows meet their deadlines using Varys in comparison to per-flow mechanisms. Moreover, Varys outperforms non-preemptive coflow schedulers by more than 5X.
Synthesis of 2,4-Di-1-pyrrolidinyl-9H-pyrimido[4,5-b]indoles, Including Antiasthma Clinical Candidate PNU-142731A (2001)

Two syntheses are described for 1-[(2,4-di-1-pyrrolidinyl-9H-pyrimido[4,5-b]indol-9-yl)-acetyl]pyrrolidine hydrochloride (PNU-142731A), a clinical candidate in the asthma area. The route involving the initial regioselective addition of glycine ethyl ester to commercially available 2,4,6-trichloropyrimidine is particularly well-suited for large-scale operation, as it is short, proceeds in good yield, is operationally straightforward, and requires no chromatographic purification of intermediates.
Transgenic goats produced by DNA pronuclear microinjection of in vitro derived zygotes (2002)

This study was undertaken to investigate various factors affecting the outcomes of in vitro fertilization (IVF) of oocytes retrieved by laparoscopic ovum pick-up (LOPU) technique from prepubertal and adult goats, as well as to evaluate the developmental competence of in vitro produced embryos. Oocyte-cumulus complexes recovered by LOPU from donors stimulated with gonadotrophins were matured in vitro. Fresh semen was used for IVF following various capacitation treatments. In vitro produced zygotes were either cultured to assess in vitro development or were transferred into recipients for full term development. The results indicated that successful IVF of the goat oocytes was affected by factors such as sperm capacitation treatment, oocyte quality, and abundance of cumulus cells on zona pellucida. Oocytes from both prepubertal and adult goats demonstrated similar full term developmental competence despite the fact that in vitro developmental rates were lower for prepubertal goats. The births of transgenic offspring demonstrated that the established LOPU-IVF technology combined with pronuclear microinjection can be successfully used to produce transgenic goats.
Critical role for the tyrosine kinase Syk in signalling through the high affinity IgE receptor of mast cells. (1996)

Activation of the high affinity IgE receptor (Fc epsilon RI) of mast cells, a member of the antigen receptor family, leads to the release of allergic mediators, a critical event in the onset of immediate hypersensitivity. Stimulation of Fc epsilon RI results in the rapid association and activation of the Syk tyrosine kinase. Using Syk-deficient mast cells we show that they fail to degranulate, synthesize leukotrienes and secrete cytokines when stimulated through Fc epsilon RI, conclusively demonstrating an essential role for Syk in Fc epsilon RI signalling. Furthermore, our data strongly supports a model of Fc epsilon RI engagement leading to the sequential activation of the tyrosine kinases Lyn and then Syk. A similar mechanism is likely to apply to signal transduction through all members of the antigen receptor family.
Essential Factors for Control of the Equilibrium in the Reversible Rearrangement of M3N@Ih‐C80 Fulleropyrrolidines: Exohedral Functional Groups versus Endohedral Metal Clusters (2014)

The effects of exohedral moieties and endohedral metal clusters on the isomerization of M3N@I(h)-C80 products from the Prato reaction through [1,5]-sigmatropic rearrangement were systematically investigated by using three types of fulleropyrrolidine derivatives and four different endohedral metal clusters. As a result, all types of derivatives provided the same ratios of the isomers for a given trimetallic nitride template (TNT) as the thermodynamic products, thus indicating that the size of the endohedral metal clusters inside C80 was the single essential factor in determining the equilibrium between the [6,6]-isomer (kinetic product) and the [5,6]-isomer. In all the derivatives, the [6,6]- and [5,6]-Prato adducts with larger metal clusters, such as Y3N and Gd3N, were equally stable, which is in good agreement with DFT calculations. The reaction rate of the rearrangement was dependent on both the substituent of exohedral functional groups and the endohedral metal-cluster size. Further DFT calculations and (13)C NMR spectroscopic studies were employed to rationalize the equilibrium in the rearrangement between the [6,6]- and [5,6]-fulleropyrrolidines.
Computer-Assisted Screening of Ziehl-Neelsen–Stained Tissue for Mycobacteria (2010)

Screening Ziehl-Neelsen (ZN)-stained sections for acid-alcohol-fast bacilli (AAFB) is laborious, and sparse bacilli are easily missed. This article presents an automatic screening algorithm using digital image analysis designed to assist human diagnosis of tissue sections. The algorithm uses multiderivative source potentiators and suppressors feeding into interconnected product nodes that result in a probability value for each image (the likelihood that it contains AAFB) and a spatial probability map showing the position of any bacillus. For the study, 3,000 images from ZN-stained tissues were captured, 1,000 were used to train the algorithm, and 2,000 were used to test it. The algorithm successfully ranked AAFB-containing images as the highest in the data sets, despite only single bacilli being present in sparse images (occupying 0.0024% of the image) and despite tissue and staining artifacts. These results suggest that this automated screening assistance method has the potential to save time and money, which is especially important in resource-poor health services.
Apoptosis, Fibrosis and Senescence (2014)

Fibrosis is a major hallmark of progressive kidney disease. The cellular mechanisms that lead to kidney tissue fibrosis are complex and include, for example, increased inflammation, increased oxidative stress, and proximal tubule cell death in the form of apoptosis or senescence. Recent studies have identified TWEAK, a tumor necrosis factor-like weak inducer of apoptosis, as a novel cytokine that mediates kidney inflammation in models of renal fibrosis. Inhibition of apoptosis via TWEAK inhibition has been shown to reduce kidney fibrosis. Recent studies using lineage tracing suggest that interstitial pericytes/perivascular fibroblasts differentiate into myofibroblasts and undergo proliferative expansion during fibrosis. Furthermore, increased expression of nuclear peroxisome proliferator-activated receptor-α in proximal tubules can directly reduce increased expression of transforming growth factor-β1 and interstitial inflammation in models of renal fibrosis, which suggests preservation of proximal tubule cell metabolism and integrity represents an important new therapeutic target. In this review, the current evidence and potential molecular mechanisms involved in the development of kidney fibrosis are discussed.
CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus (2015)

Chronic hepatitis B virus (HBV) infection is prevalent, deadly, and seldom cured due to the persistence of viral episomal DNA (cccDNA) in infected cells. Newly developed genome engineering tools may offer the ability to directly cleave viral DNA, thereby promoting viral clearance. Here, we show that the CRISPR/Cas9 system can specifically target and cleave conserved regions in the HBV genome, resulting in robust suppression of viral gene expression and replication. Upon sustained expression of Cas9 and appropriately chosen guide RNAs, we demonstrate cleavage of cccDNA by Cas9 and a dramatic reduction in both cccDNA and other parameters of viral gene expression and replication. Thus, we show that directly targeting viral episomal DNA is a novel therapeutic approach to control the virus and possibly cure patients.
In-House Characterization Technique For Steppers (1989)

This paper propose an user characterization technique for optical steppers. The purpose of such technique is to understand and to control those factors which affect stepper performances when fabrication of structures close or below the resolution specifications of the optical system is required. Two main factors are considered to limit stepper capabilities in submicron lithography: the imaging optics as a transmitter of high spatial frequencies with certain image intensity profile and the photoresist as a receiver of this optical information. The reported experiments use as the resist receiver a positive resist with a basic component added (0-4% by weight) in order to increase the resist transfer function and to decrease the K factor (from Rayleigh two points resolution criteria for isolated patterns, R = K&lambda;/N.A.). From spectral absorption of the in-house doped resist, we found that doping component concentration makes the process suitable for high resolution/ minimizing reflectivity/stepper target recognition. The imaging optics factors, a 0.31 N.A. /10X and 0.30-0.40 N.A./5X g-line steppers have been tested in the reversed resist process for linewidth change with defocus for various first/second exposure doses;exposure-defocus window;depth of focus for tangential/sagittal 1 micron lines/spaces patterns;lens capabilities to reproduce over all 10x10 mm field horizontal and vertical 1 micron lines. The latter is a useful indication in mixing-and-matching two steppers. Minimum 0.5 micron isolated patterns were reproduced in the reversed process, simultaneously in opposite polarities. The imaging optics was tested also for third order distorsion and errors of 50 ppm at optical field edges could be simply detected.
Metabolic Engineering of Escherichia coli for Enhanced Production of Succinic Acid, Based on Genome Comparison and In Silico Gene Knockout Simulation (2005)

Comparative analysis of the genomes of mixed-acid-fermenting Escherichia coli and succinic acid-overproducing Mannheimia succiniciproducens was carried out to identify candidate genes to be manipulated for overproducing succinic acid in E. coli. This resulted in the identification of five genes or operons, including ptsG, pykF, sdhA, mqo, and aceBA, which may drive metabolic fluxes away from succinic acid formation in the central metabolic pathway of E. coli. However, combinatorial disruption of these rationally selected genes did not allow enhanced succinic acid production in E. coli. Therefore, in silico metabolic analysis based on linear programming was carried out to evaluate the correlation between the maximum biomass and succinic acid production for various combinatorial knockout strains. This in silico analysis predicted that disrupting the genes for three pyruvate forming enzymes, ptsG, pykF, and pykA, allows enhanced succinic acid production. Indeed, this triple mutation increased the succinic acid production by more than sevenfold and the ratio of succinic acid to fermentation products by ninefold. It could be concluded that reducing the metabolic flux to pyruvate is crucial to achieve efficient succinic acid production in E. coli. These results suggest that the comparative genome analysis combined with in silico metabolic analysis can be an efficient way of developing strategies for strain improvement.
Levetiracetam: pharmacology and therapeutics in the treatment of epilepsy and other neurological conditions (2004)

Prior to weaning, young rabbits take up increased amounts of macromolecules across the intestine and into the circulation. The increased macromolecular uptake may be due in part to decreased intestinal proteolysis in these animals. To assess the effect of intestinal proteolysis on macromolecular uptake, we initially tested the basal level of intestinal trypsin-like activity in newborn and 4-week-old weaned animals. The newborn rabbits had significantly less trypsin-like activity in their small intestinal rinse fluid compared to the 4-week-old animals. Subsequently, we tested the effect of the protease inhibitor, aprotinin, on small intestinal rinse fluid trypsin-like activity and the intestinal uptake of bovine serum albumin (BSA). Newborn and 2-week-old rabbits were force-fed with aprotinin or phosphate-buffered saline (PBS) followed after several hours by BSA. Animals pretreated with aprotinin had significantly decreased levels of small intestinal rinse fluid trypsin-like activity and increased concentrations of immunoreactive BSA (iBSA) in plasma compared to PBS-pretreated control animals. 4-week-old weaned rabbits force-fed with equivalent amounts (on the basis of body weight) of aprotinin and BSA had significantly decreased trypsin-like activity in small intestinal rinse fluid compared to control animals. However, plasma iBSA was not significantly different from that of PBS-pretreated controls. These findings suggest that the inhibition of intestinal proteolytic activity is associated with increased macromolecular uptake in young rabbits prior to weaning. At weaning, suppression of proteolytic activity was not associated with increased macromolecular uptake detectable with the same assay procedures used successfully in the newborn animals.(ABSTRACT TRUNCATED AT 250 WORDS)
Fiber-grating external-cavity laser diode module for 2.5 Gb/s dense WDM transmission (2002)

A fiber-grating external cavity laser (FGL) module comprising semiconductor optical amplifier (SOA) with slantwise waveguide has been successfully fabricated. Advantages in application to 2.5 Gb/s dense WDM transmission have been assured.
Streamlined Completions Process: An Eagle Ford Shale Case History (2012)

Abstract The Eagle Ford shale is a hydrocarbon-producing formation of significant importance due to its capability for producing at high-liquid/gas ratios, more so than other traditional shale plays. Situated in south Texas, the total Eagle Ford liquids production in 2007 was less than 21,000 bbl total. In 2011, production averaged 65,500 BOPD in the play (EIA, 2011). Activity in the Eagle Ford continues to increase because the benefits from producing high liquid yields across much of the play, along with attractive commodity prices, have made the Eagle Ford a more attractive development over many other shale reservoirs. The rapid development of the Eagle Ford shale was enabled by horizontal drilling. In 2007 none of the reported production was from horizontal wells. In 2011 alone over 2,800 drilling permits were issued, virtually all of them for horizontal wells (RigData, 2012). The Eagle Ford shale has low-clay content, high-carbonate content, and is in an extensional basin, making it conducive to somewhat complex hydraulic fracturing (Martin et al, 2011). The plug and perforating technique has become the preferred completion method in the play due to multiple entry points creating complex fractures at a minimal cost. This completion technique requires a mechanical means for conveying perforating guns, such as coiled tubing (CT), wireline tractor or stick pipe, for the first fracturing stage at the toe of the well. To streamline their completion process, an Eagle Ford operator chose to use an initiator valve that is run at the toe of the well as part of the final completion design. This pressure activated valve is capable of initiating operations on the first fracturing stage without the need for CT or other mechanical means of conveyance of perforating guns. Simple and robust, the valve is activated by a pressure increase from the surface. The valve uses a rupture disc for precise activation and a helical port design that allows for hydraulic fracturing to be performed through the valve into the cement and the formation. With over a dozen wells completed in the Eagle Ford formation by the operator, the valve has provided logistical and economic benefits to the streamlined completion process. This paper describes the initiator valve completion tool and its application in the Eagle Ford shale. A case history is presented to show the specific design and operation of the initiator valve, as well as its benefits over other completion practices that target the first stage in a closed lateral system. Detailed activation of the valve and fracturing data through the valve are also presented.
Asn to Lys mutations at three sites which are N-glycosylated in the mammalian protein decrease the aggregation of Escherichia coli-derived erythropoietin (2001)

Erythropoietin (EPO) derived from Escherichia coli is unstable to elevated temperature and tends to aggregate with time, making it unsuitable for high-resolution structure analysis. The mammalian EPO contains about 40% carbohydrate, which makes this protein more stable and less prone to aggregate than non-glycosylated E.coli-derived EPO, but makes it unsuitable for high-resolution analysis owing to its size and flexibility. In an attempt to decrease the aggregation of E.coli-derived EPO, the three asparagine residues at positions 24, 38 and 83 were mutated to lysine residues. In the native protein, these residues are the sites of N-linked glycosylation, which suggests that they should be located on the surface of the protein and should not be involved in interactions in the hydrophobic protein core. Therefore, the substitution of basic amino acids for these neutral asparagine residues is not expected to affect the protein structure, but should increase the isoelectric point of the protein and its net positive charge, decreasing its tendency to aggregate at or below neutral pH due to electrostatic interactions. No apparent alterations in receptor binding, as determined by both cell-surface receptor competition assay and in vitro receptor dimerization experiments, were observed when these mutations were introduced into the EPO sequence. However, this mutant protein displayed a significant increase in stability to heat treatment and to storage, relative to the wild-type molecule. This resulted in a greater number of observable cross peaks in the mutant EPO in 2D NOESY experiments. However, the mutant was similar to the wild-type in stability when urea was used as a denaturant. This indicates that the introduced mutations resulted in a decrease in aggregation with heating or with prolonged incubation at ambient temperature, without changing the conformational stability or the receptor binding affinity of the mutant protein. This approach of placing charged residues at sites where N-glycosylation occurs in vivo could be applied to other systems as well.
GaAs FET RF switches (1985)

The device parameter dependences of GaAs FET switch performance have been determined analytically and by two-dimension simulation. FET switch design would maximize the value of the switch quality factor while retaining the power handling capacity. Expressions for both the quality factor and power handling capacity are derived in terms of device parameters, and would enable such optimization to be performed.
ω-3 Intake and Visual Acuity in Patients With Retinitis Pigmentosa Receiving Vitamin A (2012)

We conclude that mean annual rates of decline in distance and retinal visual acuities in adults with retinitis pigmentosa receiving vitamin A, 15 000 IU/d,are slower over 4 to 6 years among those consuming a diet rich in ω-3 fatty acids. To our knowledge, this is the first report that nutritional intake can modify the rate of decline of visual acuity in retinitis pigmentosa.
Isolation, Cloning, and Primary Structure of a Cationic 16-kDa Outer Membrane Protein of Salmonella typhimurium (1989)

By using acid-urea polyacrylamide gel electrophoresis, two cationic proteins were found in the isolated outer membranes of Salmonella typhimurium SH5014. Also, all the other enterobacterial strains studied (five additional strains of S. typhimurium, one strain of Salmonella minnesota, and three strains of Escherichia coli K12) had those proteins. The most abundant (OMB2) was purified in preparative acid-urea polyacrylamide gel electrophoresis and reversed-phase high pressure liquid chromatography (HPLC). It had a molecular mass of 16 kDa, a pI above 10.0, and was rich in arginine and lysine. 72% of the total amino acid sequence was determined by sequencing several HPLC-purified proteolytic fragments and 55 amino acids from the NH2 terminus. Furthermore, we isolated by molecular cloning the corresponding gene, named it ompH, and determined its nucleotide sequence. By combining protein and nucleotide sequence data, we determined the primary structure of the entire OmpH protein. It consists of 141 amino acids, possesses regions very rich in basic amino acids, and has a molecular mass of 15,862 kDa.
Expressing and optimizing sequence queries in database systems (2004)

The need to search for complex and recurring patterns in database sequences is shared by many applications. In this paper, we investigate the design and optimization of a query language capable of expressing and supporting efficiently the search for complex sequential patterns in database systems. Thus, we first introduce SQL-TS, an extension of SQL to express these patterns, and then we study how to optimize the queries for this language. We take the optimal text search algorithm of Knuth, Morris and Pratt, and generalize it to handle complex queries on sequences. Our algorithm exploits the interdependencies between the elements of a pattern to minimize repeated passes over the same data. Experimental results on typical sequence queries, such as double bottom queries, confirm that substantial speedups are achieved by our new optimization techniques.