gebhart/patrepeval huggingface dataset:
Regular solution model for asphaltene precipitation from bitumens and solvents (2003)

Abstract A regular solution theory liquid‐liquid equilibrium model was developed to predict asphaltene precipitation from Western Canadian bitumens. The input parameters for the model are the mole fraction, molar volume, and solubility parameters for each component. Bitumens were divided into four main pseudo‐components corresponding to SARA fractions: saturates, aromatics, resins, and asphaltenes. Asphaltenes were divided into fractions of different associated molar mass based on a Schultz‐Zimm molar mass distribution. Asphaltene self‐association was accounted for through the average molar mass of the distribution. The molar volumes and solubility parameters of the pseudo‐components were calculated using solubility, density, and molar mass measurements. The model successfully predicted the effect of solvent type and associated molar mass on asphaltene precipitation for model oil and n‐alkane systems. The model also predicted the onset and amount of asphaltene precipitation from bitumens.
User-Level Implementations of Read-Copy Update (2011)

Read-copy update (RCU) is a synchronization technique that often replaces reader-writer locking because RCU's read-side primitives are both wait-free and an order of magnitude faster than uncontended locking. Although RCU updates are relatively heavy weight, the importance of read-side performance is increasing as computing systems become more responsive to changes in their environments. RCU is heavily used in several kernel-level environments. Unfortunately, kernel-level implementations use facilities that are often unavailable to user applications. The few prior user-level RCU implementations either provided inefficient read-side primitives or restricted the application architecture. This paper fills this gap by describing efficient and flexible RCU implementations based on primitives commonly available to user-level applications. Finally, this paper compares these RCU implementations with each other and with standard locking, which enables choosing the best mechanism for a given workload. This work opens the door to widespread user-application use of RCU.
HDAC4-Regulated STAT1 Activation Mediates Platinum Resistance in Ovarian Cancer (2011)

Ovarian cancer frequently acquires resistance to platinum chemotherapy, representing a major challenge for improving patient survival. Recent work suggests that resistant clones exist within a larger drug-sensitive cell population prior to chemotherapy, implying that resistance is selected for rather than generated by treatment. We sought to compare clinically derived, intrapatient paired models of initial platinum response and subsequent resistant relapse to define molecular determinants of evolved resistance. Transcriptional analysis of a matched cell line series from three patients with high-grade serous ovarian cancer before and after development of clinical platinum resistance (PEO1/PEO4/PEO6, PEA1/PEA2, PEO14/PEO23) identified 91 up- and 126 downregulated genes common to acquired resistance. Significantly enhanced apoptotic response to platinum treatment in resistant cells was observed following knockdown of histone deacetylase (HDAC) 4, FOLR2, PIK3R1, or STAT1 (P < 0.05). Interestingly, HDAC4 and STAT1 were found to physically interact. Acetyl-STAT1 was detected in platinum-sensitive cells but not in HDAC4 overexpressing platinum-resistant cells from the same patient. In resistant cells, STAT1 phosphorylation/nuclear translocation was seen following platinum exposure, whereas silencing of HDAC4 increased acetyl-STAT1 levels, prevented platinum-induced STAT1 activation, and restored cisplatin sensitivity. Conversely, matched sensitive cells were refractory to STAT1 phosphorylation on platinum treatment. Analysis of 16 paired tumor biopsies taken before and after development of clinical platinum resistance showed significantly increased HDAC4 expression in resistant tumors [n = 7 of 16 (44%); P = 0.04]. Therefore, clinical selection of HDAC4-overexpressing tumor cells upon exposure to chemotherapy promotes STAT1 deacetylation and cancer cell survival. Together, our findings identify HDAC4 as a novel, therapeutically tractable target to counter platinum resistance in ovarian cancer.
Targeted metabolite and transcript profiling for elucidating enzyme function: isolation of novel N‐methyltransferases from three benzylisoquinoline alkaloid‐producing species (2009)

An integrated approach using targeted metabolite profiles and modest EST libraries each containing approximately 3500 unigenes was developed in order to discover and functionally characterize novel genes involved in plant-specialized metabolism. EST databases have been established for benzylisoquinoline alkaloid-producing cell cultures of Eschscholzia californica, Papaver bracteatum and Thalictrum flavum, and are a rich repository of alkaloid biosynthetic genes. ESI-FTICR-MS and ESI-MS/MS analyses facilitated unambiguous identification and relative quantification of the alkaloids in each system. Manual integration of known and candidate biosynthetic genes in each EST library with benzylisoquinoline alkaloid biosynthetic networks assembled from empirical metabolite profiles allowed identification and functional characterization of four N-methyltransferases (NMTs). One cDNA from T. flavum encoded pavine N-methyltransferase (TfPavNMT), which showed a unique preference for (+/-)-pavine and represents the first isolated enzyme involved in the pavine alkaloid branch pathway. Correlation of the occurrence of specific alkaloids, the complement of ESTs encoding known benzylisoquinoline alkaloid biosynthetic genes and the differential substrate range of characterized NMTs demonstrated the feasibility of bilaterally predicting enzyme function and species-dependent specialized metabolite profiles.
Structure-Based Design, Synthesis, and Biological Evaluation of Irreversible Human Rhinovirus 3C Protease Inhibitors. 8. Pharmacological Optimization of Orally Bioavailable 2-Pyridone-Containing Peptidomimetics (2003)

The optimization of the pharmacokinetic performance of various 2-pyridone-containing human rhinovirus (HRV) 3C protease (3CP) inhibitors following oral administration to either beagle dogs or CM-monkeys is described. The molecules described in this work are composed of a 2-pyridone-containing peptidomimetic binding determinant and an alpha,beta-unsaturated ester Michael acceptor moiety which forms an irreversible covalent adduct with the active site cysteine residue of the 3C enzyme. Modification of the ester contained within these compounds is detailed along with alteration of the P(2) substituent present in the peptidomimetic portion of the inhibitors. The pharmacokinetics of several inhibitors in both dogs and monkeys are described (7 h plasma concentrations after oral administration) along with their human plasma stabilities, stabilities in incubations with human, dog, and monkey microsomes and hepatocytes, Caco-2 permeabilities, and aqueous solubilities. Compounds containing an alpha,beta-unsaturated ethyl ester fragment and either an ethyl or propargyl P(2) moiety displayed the most promising combination of 3C enzyme inhibition (k(obs)/[I] 170 000-223 000 M(-1) s(-1)), antiviral activity (EC(50) = 0.047-0.058 microM, mean vs seven HRV serotypes), and pharmacokinetics following oral administration (7 h dog plasma levels = 0.248-0.682 microM; 7 h CM-monkey plasma levels = 0.057-0.896 microM).
Synthesis and evaluation of radioiodinated 2-(2(RS)-aminopropyl)-5-iodothiophenes as brain imaging agents (1992)

Methods have been developed for the preparation of 2-(2(RS)-aminopropyl)-5-iodothiophenes. The syntheses and physical properties of 2-(2(RS)-aminopropyl)-5-iodothiophene and N-isopropyl-2-(2(RS)-aminopropyl)-5-iodothiophene are described. The radioiodinated agents are of interest because of the high expected uptake and prolonged brain retention that may result from binding to high-capacity, relatively nonspecific amine binding sites. Radioiodine was introduced into the 5-position of 2-(2(RS)-aminopropyl)-5-iodothiophene and N-isopropyl-2-(2(RS)-aminopropyl)-5-iodothiophene by radioiodination of the corresponding 5-boronic acid or 5-(trimethylstannyl) derivatives. Tissue distribution studies in rats with 2-(2(RS)-aminopropyl)-5-[125I]iodothiophene showed high brain uptake (5 min, 2.77% dose/g; 30 min, 2.51% dose/g) and good brain/blood (B/B) ratios (5 min, 6/1; 30 min 3.8/1. A comparison of the brain uptake of the N-isopropyl derivative with the 2(RS)-aminopropyl analogue demonstrated higher initial brain uptake and brain to blood ratios (5 min, 3.2% dose/g; 10.3/1) but more rapid washout (30 min, 1.37% dose; 2.8/1). These data suggest that radiolabeled 2-(2(RS)-aminopropyl)-5-iodothiophenes are potentially useful agents for cerebral perfusion imaging by single-photon-emission computerized tomography (SPECT).
Neisseria gonorrhoeaeAntimicrobial Susceptibility Surveillance — The Gonococcal Isolate Surveillance Project, 27 Sites, United States, 2014 (2016)

Antimicrobial susceptibility surveillance is conducted to guide development of treatment recommendations for effective therapy and prevention of complications from and transmission of gonorrhea. Federal agencies can use GISP data to develop national treatment recommendations and set research and prevention priorities. Local and state health departments can use GISP data to determine allocation of STD prevention services and resources, guide prevention planning, and communicate best treatment practices to health care providers. Continued surveillance, appropriate treatment, development of new antibiotics, and prevention of transmission remain the best strategies to reduce gonorrhea incidence and morbidity.
Optimizing FPGA-based Accelerator Design for Deep Convolutional Neural Networks (2015)

Convolutional neural network (CNN) has been widely employed for image recognition because it can achieve high accuracy by emulating behavior of optic nerves in living creatures. Recently, rapid growth of modern applications based on deep learning algorithms has further improved research and implementations. Especially, various accelerators for deep CNN have been proposed based on FPGA platform because it has advantages of high performance, reconfigurability, and fast development round, etc. Although current FPGA accelerators have demonstrated better performance over generic processors, the accelerator design space has not been well exploited. One critical problem is that the computation throughput may not well match the memory bandwidth provided an FPGA platform. Consequently, existing approaches cannot achieve best performance due to under-utilization of either logic resource or memory bandwidth. At the same time, the increasing complexity and scalability of deep learning applications aggravate this problem. In order to overcome this problem, we propose an analytical design scheme using the roofline model. For any solution of a CNN design, we quantitatively analyze its computing throughput and required memory bandwidth using various optimization techniques, such as loop tiling and transformation. Then, with the help of rooine model, we can identify the solution with best performance and lowest FPGA resource requirement. As a case study, we implement a CNN accelerator on a VC707 FPGA board and compare it to previous approaches. Our implementation achieves a peak performance of 61.62 GFLOPS under 100MHz working frequency, which outperform previous approaches significantly.
Paclitaxel triggers cell death primarily via caspase-independent routes in the non-small cell lung cancer cell line NCI-H460. (2002)

Paclitaxel triggers cell death in H460 cells mainly via a currently unidentified caspase-independent mechanism in which the basic apoptotic machinery is merely coactivated. This finding is in sharp contrast with the largely caspase-dependent response elicited by DNA-damaging agents in these cells. We speculate on therapeutic implications.
Halorhodopsin is a light-driven chloride pump. (1982)

Light-dependent membrane potentials, ionic fluxes, and volume changes were measured in two kinds of Halobacterium halobium cell envelope vesicles: one containing bacteriorhodopsin and another halorhodopsin. Bacteriorhodopsin-containing vesicles extruded protons by a primary electrogenic mechanism and an energized volume decrease was observed. This was shown to be the consequences of sodium extrusion via proton/sodium antiport (which recirculated protons) and the accompanying passive chloride extrusion. Halorhodopsin-containing vesicles, in contrast, exhibited a volume increase during illumination, apparently caused by primary inward transport of chloride, and accompanied by passive cation (sodium or potassium, and proton) uptake. It was demonstrated that the chloride transport will occur against both electrical and concentration gradients across the vesicle membrane. Moreover, chloride was required on the vesicle exterior for the light-dependent generation of membrane potential, pH change, and swelling. These observations are inconsistent with an earlier proposal that halorhodopsin is an outward directed sodium pump, but suggest very strongly that it is an inward directed chloride pump. Quantitative arguments from the present work rule out a significant role of sodium in the functioning of halorhodopsin.
Towards a multimodal meeting record (2002)

Face-to-face meetings usually encompass several modalities including speech, gesture, handwriting, and person identification. Recognition and integration of each of these modalities is important to create an accurate record of a meeting. However, each of these modalities presents recognition difficulties. Speech recognition must be speaker and domain independent, have low word error rates, and be close to real time to be useful. Gesture and handwriting recognition must be writer independent and support a wide variety of writing styles. Person identification has difficulty with segmentation in a crowded room. Furthermore, in order to produce the record automatically, we have to solve the assignment problem (who is saying what), which involves people identification and speech recognition. This paper examines a multimodal meeting room system under development at Carnegie Mellon University that enables us to track, capture and integrate the important aspects of a meeting from people identification to meeting transcription. Once a multimedia meeting record is created, it can be archived for later retrieval.
Reinforced Video Captioning with Entailment Rewards (2017)

Sequence-to-sequence models have shown promising improvements on the temporal task of video captioning, but they optimize word-level cross-entropy loss during training. First, using policy gradient and mixed-loss methods for reinforcement learning, we directly optimize sentence-level task-based metrics (as rewards), achieving significant improvements over the baseline, based on both automatic metrics and human evaluation on multiple datasets. Next, we propose a novel entailment-enhanced reward (CIDEnt) that corrects phrase-matching based metrics (such as CIDEr) to only allow for logically-implied partial matches and avoid contradictions, achieving further significant improvements over the CIDEr-reward model.
Effect of &gt;100&lt; channel direction for high performance SCE immune pMOSFET with less than 0.15 μm gate length (2003)

A high performance CMOSFET with a channel along the <100> crystallographic axis has been developed. Current drivability of the pMOSFET is improved by about 15% by changing the channel direction from <110> to <100> due to an increase in hole mobility and high immunity against short channel effects (SCE). As a result, a drive current of 810 /spl mu/A//spl mu/m for nMOS and of 420 /spl mu/A//spl mu/m for pMOS with 0.14 /spl mu/m gate length has been achieved under 1 nA//spl mu/m off current at 1.8 V operation.
Strained Si surface channel MOSFETs for high-performance CMOS technology (2002)

Biaxial tension enhances in-plane transport of both electrons and holes in silicon, and can improve the current drive of CMOS devices independent of geometric scaling and electrostatic design. Device performance enhancements and issues to be addressed before the realization of strained Si CMOS technology are discussed.
Inhalation of the Nitric Oxide Synthase Cofactor Tetrahydrobiopterin in Healthy Volunteers (1997)

Pulmonary endothelial dysfunction is the hallmark of acute lung injury. Impaired pulmonary endothelial nitric oxide (NO) production in this event has been described. Tetrahydrobiopterin (BH4) is an essential cofactor for NO synthase and modulator of its activity. At high local concentrations, BH4 provokes local vasodilation in vivo in healthy individuals. At lower concentrations, BH4 selectively and locally restores disturbed NO-dependent vasodilation in patients with endothelial dysfunction. In this preliminary study, we therefore investigated the feasibility of BH4 inhalation in five healthy human volunteers. Inhalation of buffered, aqueous BH4-dihydrochloride solution was well tolerated; despite the buffer, BH4 stability was completely preserved. Resorption of inhaled BH4 was demonstrated by significantly increased BH4 levels in plasma and urine. Inhaled BH4 did not alter pulmonary function and had no effect on systemic hemodynamic values. Our data demonstrate that inhalation is a novel method for local BH4 administration, offering a basic therapeutic tool for investigation of restoration of impaired NO-dependent vasodilation due to pulmonary endothelial dysfunction.
Glycolipid Antigen Drives Rapid Expansion and Sustained Cytokine Production by NK T Cells (2003)

Abstract NKT cells are enigmatic lymphocytes that respond to glycolipid Ags presented by CD1d. Although they are key immunoregulatory cells, with a critical role in immunity to cancer, infection, and autoimmune diseases, little is known about how they respond to antigenic challenge. Current theories suggest that NKT cells die within hours of stimulation, implying that their direct impact on the immune system derives from the initial cytokine burst released before their death. Here we show that NKT cell disappearance results from TCR down-regulation rather than apoptosis, and that they expand to many times their normal number in peripheral tissues within 2–3 days of stimulation, before contracting to normal numbers over subsequent days. This expansion is associated with ongoing cytokine production, biased toward a Th1 (IFN-γ+ IL-4−) phenotype, in contrast to their initial Th0 (IFN-γ+IL-4+) phenotype. This study provides critical new insight into how NKT cells can have such a major impact on immune responses, lasting many days beyond the initial stimulation of these cells.
Representing discourse coherence (2004)

We present a set of discourse structure relations that are easy to code, and develop criteria for an appropriate data structure for representing these relations. Discourse structure here refers to informational relations that hold between sentences in a discourse (cf. Hobbs, 1985). We evaluated whether trees are a descriptively adequate data structure for representing coherence. Trees are widely assumed as a data structure for representing coherence but we found that more powerful data structures are needed: In coherence structures of naturally occurring texts, we found many different kinds of crossed dependencies, as well as many nodes with multiple parents. The claims are supported by statistical results from a database of 135 texts from the Wall Street Journal and the AP Newswire that were hand-annotated with coherence relations, based on the annotation schema presented in this paper.
Highly Efficient Synthesis of Functionalized Indolizines and Indolizinones by Copper-Catalyzed Cycloisomerizations of Propargylic Pyridines (2007)

The copper-catalyzed cycloisomerizations of 2-pyridyl-substituted propargylic acetates and its derivatives are described, which offer an efficient route to C-1 oxygenated indolizines with a wide range of substituents under mild reaction conditions. The presented method could be readily applied to the synthesis of indolizinones through a cyclization/1,2-migration of tertiary propargylic alcohols.
Streptococcus pneumoniae Endohexosaminidase D, Structural and Mechanistic Insight into Substrate-assisted Catalysis in Family 85 Glycoside Hydrolases (2009)

Endo-beta-d-glucosaminidases from family 85 of glycoside hydrolases (GH85 endohexosaminidases) act to cleave the glycosidic linkage between the two N-acetylglucosamine units that make up the chitobiose core of N-glycans. Endohexosaminidase D (Endo-D), produced by Streptococcus pneumoniae, is believed to contribute to the virulence of this organism by playing a role in the deglycosylation of IgG antibodies. Endohexosaminidases have received significant attention for this reason and, moreover, because they are powerful tools for chemoenzymatic synthesis of proteins having defined glycoforms. Here we describe mechanistic and structural studies of the catalytic domain (SpGH85) of Endo-D that provide compelling support for GH85 enzymes using a catalytic mechanism involving substrate-assisted catalysis. Furthermore, the structure of SpGH85 in complex with the mechanism-based competitive inhibitor NAG-thiazoline (K(d) = 28 microm) provides a coherent rationale for previous mutagenesis studies of Endo-D and other related GH85 enzymes. We also find GH85, GH56, and GH18 enzymes have a similar configuration of catalytic residues. Notably, GH85 enzymes have an asparagine in place of the aspartate residue found in these other families of glycosidases. We propose that this residue, as the imidic acid tautomer, acts analogously to the key catalytic aspartate of GH56 and GH18 enzymes. This topographically conserved arrangement of the asparagine residue and a conserved glutamic acid, coupled with previous kinetic studies, suggests these enzymes may use an unusual proton shuttle to coordinate effective general acid and base catalysis to aid cleavage of the glycosidic bond. These results collectively provide a blueprint that may be used to facilitate protein engineering of these enzymes to improve their function as biocatalysts for synthesizing glycoproteins having defined glycoforms and also may serve as a guide for generating inhibitors of GH85 enzymes.
High-resolution aluminum-27 NMR of aluminosilicates (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHigh-resolution aluminum-27 NMR of aluminosilicatesE. Lippmaa, A. Samoson, and M. MagiCite this: J. Am. Chem. Soc. 1986, 108, 8, 1730–1735Publication Date (Print):April 1, 1986Publication History Published online1 May 2002Published inissue 1 April 1986https://pubs.acs.org/doi/10.1021/ja00268a002https://doi.org/10.1021/ja00268a002research-articleACS PublicationsRequest reuse permissionsArticle Views2184Altmetric-Citations518LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts