gebhart/patrepeval huggingface dataset:
Washout of Cr(III)-Acetate-HPAM Gels from Fractures (2003)

Abstract This paper investigates washout of mature Cr(III)-acetate-HPAM gels from fractures. After gel placement, the pressure gradient for gel washout during brine or oil flow was similar to the pressure gradient observed during gel placement. The mechanism of gel failure involved the displacement of relatively mobile gel from wormholes. Generally, only a small fraction of the gel (&lt;5%) was displaced during the washout process. Resistance to washout can be increased by injecting a more concentrated gel. However, this approach exhibits significantly higher pressure gradients during gel placement. The presence of a constriction in a fracture inhibited gel washout during the first pulse of brine flow after gel placement. However, during subsequent brine flow, gel erosion occurred upstream of the constriction to the same extent as downstream. The extrusion, leakoff, and washout behavior in fractures in strongly oil-wet polyethylene cores were similar to those in strongly water-wet Berea sandstone. Gel washout can be reduced by controlling gel placement rate. A Cr(III)-acetate-HPAM gel placed in a 0.04-in. wide fracture at 826 ft/d was about five times more resistant to washout than a gel placed at 4,130 ft/d. Gel washout can also be reduced using secondary crosslinking reactions. Post-placement reaction with Cr(III) acetate increased resistance to washout for a resorcinol-formaldehyde-HPAM gel by a factor from two to three. During steady state flow after first breaching the gel, a Cr(III)-acetate-HPAM gel reduced permeability to water (within the fracture) moderately more (2.5 to 4.7 times) than that to oil. Disproportionate permeability reduction in fractures was most evident at low flow rates.
Series-coupled silicon racetrack resonators and the Vernier effect: theory and measurement (2010)

Silicon-on-insulator racetrack resonators can be used as multiplexers in wavelength division multiplexing applications. The free spectral range should be comparable to the span of the C-band so that a maximum number of channels can be multiplexed. However, the free spectral range is inversely proportional to the length of the resonator and, therefore, bending losses can become non-negligible. A viable alternative to increase the free spectral range is to use the Vernier effect. In this work, we present the theory of series-coupled racetrack resonators exhibiting the Vernier effect. We demonstrate the experimental performance of the device using silicon-on-insulator strip waveguides. The extended free spectral range is 36 nm and the interstitial peak suppression is from 9 dB to 17 dB.
Spatially Localized Atlas Network Tiles Enables 3D Whole Brain Segmentation from Limited Data (2018)

Whole brain segmentation on a structural magnetic resonance imaging (MRI) is essential in non-invasive investigation for neuroanatomy. Historically, multi-atlas segmentation (MAS) has been regarded as the de facto standard method for whole brain segmentation. Recently, deep neural network approaches have been applied to whole brain segmentation by learning random patches or 2D slices. Yet, few previous efforts have been made on detailed whole brain segmentation using 3D networks due to the following challenges: (1) fitting entire whole brain volume into 3D networks is restricted by the current GPU memory, and (2) the large number of targeting labels (e.g., > 100 labels) with limited number of training 3D volumes (e.g., < 50 scans). In this paper, we propose the spatially localized atlas network tiles (SLANT) method to distribute multiple independent 3D fully convolutional networks to cover overlapped sub-spaces in a standard atlas space. This strategy simplifies the whole brain learning task to localized sub-tasks, which was enabled by combing canonical registration and label fusion techniques with deep learning. To address the second challenge, auxiliary labels on 5111 initially unlabeled scans were created by MAS for pre-training. From empirical validation, the state-of-the-art MAS method achieved mean Dice value of 0.76, 0.71, and 0.68, while the proposed method achieved 0.78, 0.73, and 0.71 on three validation cohorts. Moreover, the computational time reduced from > 30 hours using MAS to ~15 minutes using the proposed method. The source code is available online https://github.com/MASILab/SLANTbrainSeg
Temperature and injection level dependencies and impact of thermal oxidation on carrier lifetimes in p-type and n-type 4H–SiC epilayers (2011)

Dependencies of temperature and injection level on carrier lifetimes in 50 μm thick p-type and n-type 4H–SiC epilayers have been investigated. The carrier lifetimes have been measured by differential microwave photoconductance decay measurements at various injection levels and temperatures. In both p-type and n-type epilayers, the carrier lifetimes gradually increased with increasing the injection level, which were naturally expected from the Shockley-Read-Hall (SRH) model, and after taking a maximum, the lifetimes dropped at the very high-injection level. In contrast, the carrier lifetimes exhibited continuous increase with elevating the temperature for both epilayers. In addition, the impact of thermal oxidation process on the carrier lifetimes has been also investigated. The thermal oxidation process, by which the Z1/2 and EH6/7 centers were remarkably reduced that had been observed in n-type 4H–SiC in our previous work, led to the improvement of the carrier lifetimes especially for n-type epilayers. The carrier lifetime reached 4.1 μs in p-type and 6.1 μs in n-type epilayers at 250 °C with an injection level of 1.8×1016 cm−3 through the thermal oxidation processing.
CD4‐mediated functional activation of human CD4<sup>+</sup>CD25<sup>+</sup> regulatory T cells (2007)

Naturally occurring CD4(+)CD25(+)FoxP3(+) regulatory T cells (CD25(+) Tregs) constitute a specialized population of T cells that is essential for the maintenance of peripheral self-tolerance. The immune regulatory function of CD25(+) Tregs depends upon their activation. We found that anti-CD4 antibodies activate the suppressive function of human CD25(+) Tregs in a dose-dependent manner. We demonstrate that CD4-activated CD25(+) Tregs suppress the proliferation of CD4(+) and CD8(+) T cells, their IL-2 and IFN-gamma production as well as the capacity of CD8(+) T cells to re-express CD25. By contrast, anti-CD4 stimulation did not induce suppressive activity in conventional CD4(+) T cells. These results identify CD4 as a trigger for the suppressive function of CD25(+) Tregs and suggest a possible CD4-mediated exploitation of these cells.
Catalytic Carbonyl Addition through Transfer Hydrogenation: A Departure from Preformed Organometallic Reagents (2008)

Classical protocols for carbonyl allylation, propargylation and vinylation typically rely upon the use of preformed allyl metal, allenyl metal and vinyl metal reagents, respectively, mandating stoichiometric generation of metallic byproducts. Through transfer hydrogenative C-C coupling, however, carbonyl addition may be achieved from the aldehyde or alcohol oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. Here, we review transfer hydrogenative methods for carbonyl addition, which encompass the first catalytic protocols enabling direct C-H functionalization of alcohols.
mTOR‐STAT3‐notch signalling contributes to ALDH2‐induced protection against cardiac contractile dysfunction and autophagy under alcoholism (2011)

Mitochondrial aldehyde dehydrogenase-2 (ALDH2) has been shown to benefit myopathic changes following alcohol intake, although the precise mechanism is still unclear. This study was designed to evaluate the role of ALDH2 on chronic alcohol intake-induced myocardial geometric and functional damage with a focus on autophagic signalling. Wild-type friendly virus B (FVB) and transgenic mice overexpressing ALDH2 driven by chicken β-actin promoter were fed a 4% alcohol liquid diet for 12 weeks. Cardiac geometry and function were assessed using echocardiographic and IonOptix systems. Western blot analysis was used to evaluate the essential autophagy markers, Akt and AMP-dependent protein kinase (AMPK) as well as their downstream signalling mammalian target of rapamycin (mTOR) and signal transducer and activator of transcription 3 (STAT3). Alcohol intake altered cardiac geometry and function as demonstrated by lessened LV wall and septal thickness, enlarged end systolic and diastolic diameters, decreased fractional shortening and cell shortening, the effects of which were mitigated by ALDH2 transgene. Chronic alcohol intake triggered myocardial autophagy as shown by LC3B II isoform switch, as well as decreased phosphorylation of mTOR, the effects of which were ablated by ALDH2. Chronic alcohol intake suppressed phosphorylation of Akt and AMPK, which was reconciled by ALDH2. Levels of Notch1 and STAT3 phosphorylation were dampened by chronic alcohol intake in FVB but not ALDH2 myocardium. Moreover, the γ-secretase Notch inhibitor N\xE2\x80\x90[N-(3,5-difluorophenacetyl)-1-alany1]-S-phenyglycine t-butyl ester exacerbated ethanol-induced cardiomyocyte contractile dysfunction, apoptosis and autophagy. In summary, these findings suggested that ALDH2 elicits cardioprotection against chronic alcohol intake-induced cardiac geometric and functional anomalies by inhibition of autophagy possibly via restoring the Akt-mTOR-STAT3-Notch signalling cascade.
Analysis of IL-1 and TNF-<i>alpha</i> gene expression in human rheumatoid synoviocytes and normal monocytes by in situ hybridization. (1990)

Abstract Human IL-1 alpha, IL-1 beta, and TNF-alpha mRNA expression was examined in peripheral blood monocytes (PBM) from normal individuals and in primary synoviocytes isolated from patients with rheumatoid arthritis by Northern blot and in situ hybridization. Cells cultured in the presence or absence of LPS were analyzed using in vitro synthesized 35S-labeled sense or antisense RNA probes to determine the relative abundance and the cell type expressing each of the mRNA for these potent inflammatory mediators. The results indicated that 72% of the LPS-stimulated PBM expressed detectable levels of IL-1 alpha mRNA, 89% IL-1 beta mRNA, and 10% TNF-alpha transcripts. Thus, the majority of activated PBM produced both IL-1 alpha and IL-1 beta. Experiments combining immunofluorescence for IL-1 beta protein with in situ hybridization for TNF-alpha mRNA demonstrated that monocytes expressing TNF-alpha mRNA also produced IL-1 beta. Primary synoviocytes from four patients with RA were also examined for the mRNA expression of each cytokine. Northern blot analyses of total RNA isolated from 0 to 72 h after LPS- or mock-stimulation showed that IL-1 beta mRNA was the most abundantly expressed, followed by TNF-alpha. In situ hybridization revealed that IL-1 beta and TNF-alpha transcripts were detected exclusively in synovial tissue macrophages. IL-1 alpha mRNA was not detected in these cultures by either method.
Inferring the Location and Effect of Tumor Suppressor Genes by Instability‐Selection Modeling of Allelic‐Loss Data (2000)

Cancerous tumor growth creates cells with abnormal DNA. Allelic-loss experiments identify genomic deletions in cancer cells, but sources of variation and intrinsic dependencies complicate inference about the location and effect of suppressor genes; such genes are the target of these experiments and are thought to be involved in tumor development. We investigate properties of an instability-selection model of allelic-loss data, including likelihood-based parameter estimation and hypothesis testing. By considering a special complete-data case, we derive an approximate calibration method for hypothesis tests of sporadic deletion. Parametric bootstrap and Bayesian computations are also developed. Data from three allelic-loss studies are reanalyzed to illustrate the methods.
SOIL MOISTURE-BASED IRRIGATION CONTROL TO CONSERVE WATER AND NUTRIENTS UNDER DRIP IRRIGATED VEGETABLE PRODUCTION (2015)

ABSTRACT. Plastic mulch and drip irrigation are commonly used in high intensity vegetable production regions such as Florida. Drip irrigation can be much more efficient than sprinkler irrigation since only the root zone of the cropped area is irrigated. However, improper irrigation management can lead to wasted water and leaching of soluble chemicals such as nitrate. The objectives of this project were to optimize tomato and green bell pepper yield under varying levels of soil moisture controlled drip irrigation. Three nitrogen rates (80%, 100%, and 150 % of the recommended rate) and several irrigation treatments were imposed on drip irrigated tomato and pepper. Irrigation treatments included soil water based automatic treatments set at 10% volumetric water content (VWC; field capacity) and 13%
Colonic secretory effect in response to enteral feeding in humans. (1994)

Diarrhoea complicating enteral feeding is a common clinical problem affecting up to 25% of patients. Its pathogenesis remains unknown. A new technique of human in vivo segmental colonic perfusion was used to investigate colonic water and electrolyte movement in response to enteral feeding. Four groups of studies were performed in which low and high load polymeric enteral diet infusions were undertaken, either intragastrically or intraduodenally (n = 6 each group). Net absorption of sodium, chloride, and water occurred during fasting throughout the colon in all groups. There was a significant net secretion of sodium, chloride, and water in the ascending colon during low load (sodium: -42 mmol/h; 95% confidence limits -52 to -19, Chloride: -18 mmol/h; -50 to +16, water: -174 ml/h; -348 to -30) and high load (sodium: -24 mmol/h; -60 to +8, chloride: -18 mmol/h; -31 to +16, water: -120 ml/h; -246 to +6) gastric feeding, and during high load duodenal feeding (sodium: -12 mmol/h; -22 to -6, chloride; -6 mmol/h; -16 to +3, water: -72 ml/h; -144 to -6). Net secretion persisted in the distal colon only during high load gastric feeding. In the other three groups there was a net absorption in the distal colon. This study identified a significant colonic secretory response to enteral feeding, which is related to the site and load of the diet infusion. This response may play an important part in the pathogenesis of enteral feeding related diarrhoea.
Allosteric Control of Acetylcholinesterase Activity by Monoclonal Antibodies (1998)

Previous studies showed that monoclonal antibodies raised against phosphorylated fetal bovine serum acetylcholinesterase appeared to modulate the catalytic activity of the enzyme by binding to a conformational epitope located at or near the region of the peripheral anionic site. The mechanism of inhibition of acetylcholinesterase by these monoclonal antibodies was further investigated by determining their effect on (i) substrate inhibition due to the binding of excess substrate to the peripheral anionic site and (ii) binding of peripheral anionic site ligands, such as propidium and fasciculin. Results of these experiments demonstrate that the accessibility of substrate to the peripheral anionic site in these complexes was restricted but not completely blocked, as none of the monoclonal antibodies eliminated the phenomenon of excess substrate inhibition. The results also show that propidium clearly slowed the inhibition of fetal bovine serum acetylcholinesterase by all six inhibitory monoclonal antibodies but to different levels. Complexation of fetal bovine serum acetylcholinesterase with monoclonal antibodies 25B1, 4E5, 6H9, and 5E8 interfered with the binding of fasciculin to the complexed enzyme, suggesting that part of their epitope overlapped with the fasciculin binding site. These monoclonal antibodies bind, in part, at the peripheral anionic site, since polyclonal anti-idiotypic antibodies generated against two monoclonal antibodies, 25B1 and 6H9, bound stoichiometric amounts of propidium. Like fasciculin, binding of these monoclonal antibodies in the vicinity of the peripheral anionic site at the rim of the active site gorge allosterically affects the orientation of W86 located at the base of the gorge, resulting in inhibition of enzyme activity.
Reduction of temperature coefficient of frequency in LiTaO<inf>3</inf> single crystals for surface acoustic wave applications (2012)

Temperature coefficient of frequency of LiTaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> single crystals was tuned by changing the Li stoichiometry. For this purpose, congruent 36°Y cut crystals, available commercially, were treated by vapor transport equilibration and temperature coefficient of frequency of surface acoustic waves propagating along X-axis as a function of Li concentration was studied. The temperature coefficient of frequency of -7 ppm/° was achieved for surface acoustic waves propagating in the crystals containing 49.43 mol % of Li <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O.
1745 and After; A Servant of the Crown (1938)

1745 and After; A Servant of the Crown 1745 and After . By Alistair and Henrietta Tayler . Nelson. 12 s . 6 d . A Servant of the Crown . By Norreys Jephson O'conor . The D. Appleton-Century Co. 12 s . 6 d . D. M. Stuart D. M. Stuart Search for other works by this author on: Oxford Academic Google Scholar English: Journal of the English Association, Volume 2, Issue 9, 1938, Pages 190–191, https://doi.org/10.1093/english/2.9.190 Published: 01 December 1938
<i>Francisella tularensis</i>regulates autophagy-related host cell signaling pathways (2009)

The Gram-negative intracellular pathogen Francisella tularensis is known for its ability to dampen host immune responses. We recently performed a microarray analysis comparing human monocyte responses to the highly virulent F. tularensis tularensis Schu S4 strain (F.t.) versus the less virulent F. tularensis novicida (F.n.).(1) Many groups of genes were affected, including those involved with autophagy and with the regulation of autophagy. Here, we discuss the implications in the context of Francisella virulence and host cell response, then conclude with potential future experiments.
Let there be light! (2011)

Energy consumption is the fundamental barrier to exascale supercomputing and it is dominated by the cost of moving data from one point to another, not computation. Similarly, performance is dominated by data movement, not computation. The solution to this problem requires three critical technologies: 3D integration, optical chip-to-chip communication, and a new communication model. A memory system based on these technologies has the potential to lower the cost of local memory accesses by orders of magnitude and provide substantially more bandwidth. To reach the goals of exascale computing with a manageable power budget, the industry will have to adopt these technologies. Doing so will enable exascale computing, and will have a major worldwide economic impact.
CONTENTS OF VOL. FOR 1839 (2013)

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Quantification and fatty acid and fatty aldehyde composition of ethanolamine, choline, and serine glycerophosphatides in human cerebral grey and white matter (1964)

The quantities of ethanolamine glycerophosphatides (EGP), choline glycerophosphatides (CGP), and serine glycerophosphatides (SGP) were determined in the grey and white matter from three apparently normal adult human brains. In each locale the quantities decreased from EGP through CGP to SGP.The quantities of aldehydes in these lipids were also determined. In grey matter the aldehyde content (expressed as per cent of fatty acids plus aldehydes) of EGP, CGP, and SGP was 22, 0.3, and 0.2% respectively; while in white matter the proportions were 49, 0.8, and 13%, respectively. Palmitaldehyde, stearaldehyde, and olealdehyde made up 90% of the aldehydes found. White matter glycerophosphatides contained much more olealdehyde than those from grey matter.EGP and SGP contained much larger proportions of C20 and C22 polyenoic acids from grey matter than from white matter. CGP, on the other hand, had a similar fatty acid composition, comprised mainly of 16:0, 18:0, and 18:1 acids, in each locale. The differences in fatty acid composition of these three glycerophosphatides may be related to the higher myelin content of white matter.
mRNA isolation in a microfluidic device for eventual integration of cDNA library construction (2000)

mRNA isolation for the purpose of cDNA library construction was performed in a microfluidic chip device using paramagnetic oligo-dT beads. The simple Y-intersection flow design mixes beads and sample on-chip, and uses magnetic trapping to capture, then release the beads. The capillary gel electrophoresis (CGE) detection of the total unamplified mRNA isolated on-chip, and of a reverse transcription-polymerase chain reaction (RT-PCR) amplified rare gene indicated that mRNA could be captured by oligo-dT beads on-chip, had very good integrity and was suitable for constructing a cDNA library. The limit of detection for the rare bicoid gene of Drosophila Melanogaster corresponded to the capture of approximately 2.8 ng of total mRNA from 0.85 microgram of total RNA (TRNA) within the microchip. As much as 34 ng of total mRNA was estimated to be captured from 10 micrograms of TRNA.
Assembly and Characterization of Biomolecule–Gold Nanoparticle Conjugates and Their Use in Intracellular Imaging (2005)

In this chapter, we outline protocols for assembling and characterizing peptide-gold nanoparticle conjugates. We describe two strategies for attaching peptides to gold nanoparticles. One involves the covalent coupling of cysteine-terminated peptides directly to a particle surface via a sulfur-gold bond. Alternatively, peptides are coupled to bovine serum albumin (BSA) via a bifunctional molecular crosslinker. We also describe a number of characterization methods for determining the number of crosslinkers per BSA, peptides per BSA, and peptides adsorbed per particle. Finally, we show that the enormous visible light extinction properties of gold nano particles make them excellent imaging agents for tracking the trajectories of peptides inside living cells.
Gene structure of human mitochondrial ATP synthase gamma-subunit. Tissue specificity produced by alternative RNA splicing. (1993)

We completely sequenced the human gene for ATP synthase gamma-subunit, which was approximately 23 kilobases long and was composed of 10 exons. Exons 1 and 2 encoded the N-terminal presequence required for mitochondrial import, while exons 9 and 10 encoded the C-terminal portions of mature protein. Enzymatic amplification of human heart and liver cDNAs using the polymerase chain reaction revealed two mRNA transcripts that were predicted to encode two 30-kDa isoforms of the gamma-subunit, which differed by the addition of a single amino acid (Asp273) at the C terminus of the liver type isoform. These two mRNA transcripts of the heart (H) type and liver (L) type were generated by alternative splicing of an exon. The same alternative splicing event was observed in bovine tissue. In human tissues, the H type mRNA devoid of exon 9 was expressed specifically in the heart and skeletal muscle, which require rapid energy supply. The L type mRNA was expressed in the brain, liver, kidney etc. Both transcripts were expressed in the skin, intestine, stomach, and aorta. This tissue specificity of transcript heterogeneity suggests the distinct functional or regulatory roles of the gamma-subunit isoforms in the catalysis of ATP synthase. This is the first report on tissue-specific isoforms generated by alternative splicing in an energy transducing mitochondrial protein.