gebhart/patrepeval huggingface dataset:
Historical Developments in Hydroprocessing Bio-oils (2007)

This paper is a review of the developments in the field of catalytic hydroprocessing of biomass-derived liquefaction conversion products (bio-oil) over the past 25 years. Work has been underway, primarily in the U.S. and Europe, in catalytic hydrotreating and hydrocracking of bio-oil in both batch-fed and continuous-flow bench-scale reactor systems. A range of heterogeneous catalyst materials have been tested, including conventional sulfided catalysts developed for petroleum hydroprocessing and precious metal catalysts. The important processing differences have been identified, which required adjustments to conventional hydroprocessing as applied to petroleum feedstocks. This application of hydroprocessing is seen as an extension of petroleum processing and system requirements are not far outside the range of conventional hydroprocessing. The technology is still under development but can play a significant role in supplementing increasingly expensive petroleum.
Reduced representation of matrices generated by the method of moments (2002)

In this paper, an algorithm is presented that accelerates the iterative solution of boundary integral equations. The matrices generated in the MoM discretization of boundary integral equations exhibit special properties, which are exploited in the proposed algorithm. In fact, the algorithm does not require the computation of the entire MoM matrix, but, rather, only calls for the computation of a judiciously selected, small set of elements of the original matrix. As a consequence, the algorithm can easily be incorporated into existing MoM codes. We show that knowledge of the set of elements suffices to compute the product of the dense MoM matrix and a trial solution vector. A single-stage version of the algorithm reduces the computational cost of a matrix-vector multiplication from O(N/sup 2/) to at least O(N/sup 1.5/), and a multi-stage version further reduces the cost, in principle, to O(NlogN). The proposed algorithm is motivated by the fact that the fields in an observation domain due to sources in a 'well separated' source domain can be represented in terms of the fields radiated by a reduced set of equivalent sources. The number of sources in the reduced set is directly related to the number of degrees of freedom (DOF) of the field radiated by the original set in the direction of the observation domain. The algorithm exhibits similarities with the multilevel algorithm proposed by Brandt (1991).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
bHLH Transcription Factor Olig1 Is Required to Repair Demyelinated Lesions in the CNS (2004)

Olig1 and Olig2 are closely related basic helix-loop-helix (bHLH) transcription factors that are expressed in myelinating oligodendrocytes and their progenitor cells in the developing central nervous system (CNS). Olig2 is necessary for the specification of oligodendrocytes, but the biological functions of Olig1 during oligodendrocyte lineage development are poorly understood. We show here that Olig1 function in mice is required not to develop the brain but to repair it. Specifically, we demonstrate a genetic requirement for Olig1 in repairing the types of lesions that occur in patients with multiple sclerosis.
Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome (2011)

Bridging the gap between animal or in vitro models and human disease is essential in medical research. Researchers often suggest that a biological mechanism is relevant to human cancer from the statistical association of a gene expression marker (a signature) of this mechanism, that was discovered in an experimental system, with disease outcome in humans. We examined this argument for breast cancer. Surprisingly, we found that gene expression signatures-unrelated to cancer-of the effect of postprandial laughter, of mice social defeat and of skin fibroblast localization were all significantly associated with breast cancer outcome. We next compared 47 published breast cancer outcome signatures to signatures made of random genes. Twenty-eight of them (60%) were not significantly better outcome predictors than random signatures of identical size and 11 (23%) were worst predictors than the median random signature. More than 90% of random signatures >100 genes were significant outcome predictors. We next derived a metagene, called meta-PCNA, by selecting the 1% genes most positively correlated with proliferation marker PCNA in a compendium of normal tissues expression. Adjusting breast cancer expression data for meta-PCNA abrogated almost entirely the outcome association of published and random signatures. We also found that, in the absence of adjustment, the hazard ratio of outcome association of a signature strongly correlated with meta-PCNA (R(2) = 0.9). This relation also applied to single-gene expression markers. Moreover, >50% of the breast cancer transcriptome was correlated with meta-PCNA. A corollary was that purging cell cycle genes out of a signature failed to rule out the confounding effect of proliferation. Hence, it is questionable to suggest that a mechanism is relevant to human breast cancer from the finding that a gene expression marker for this mechanism predicts human breast cancer outcome, because most markers do. The methods we present help to overcome this problem.
Hemorrhagic Fever Viruses as Biological Weapons (2002)

Weapons disseminating a number of HFVs could cause an outbreak of an undifferentiated febrile illness 2 to 21 days later, associated with clinical manifestations that could include rash, hemorrhagic diathesis, and shock. The mode of transmission and clinical course would vary depending on the specific pathogen. Diagnosis may be delayed given clinicians' unfamiliarity with these diseases, heterogeneous clinical presentation within an infected cohort, and lack of widely available diagnostic tests. Initiation of ribavirin therapy in the early phases of illness may be useful in treatment of some of these viruses, although extensive experience is lacking. There are no licensed vaccines to treat the diseases caused by HFVs.
Interlocked and Intertwined Structures and Superstructures (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleInterlocked and Intertwined Structures and SuperstructuresDavid B. Amabilino and J. Fraser StoddartCite this: Chem. Rev. 1995, 95, 8, 2725–2828Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://doi.org/10.1021/cr00040a005RIGHTS & PERMISSIONSArticle Views8218Altmetric-Citations1371LEARN 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 InReddit PDF (35 MB) Get e-Alerts Get e-Alerts
Analysis of transcriptional activity mediated by Drosophila melanogaster ecdysone receptor isoforms in a heterologous cell culture system (2006)

Ecdysteroid regulation of gene transcription in Drosophila melanogaster and other insects is mediated by a heterodimer comprised of Ultraspiracle (USP) and one of three ecdysone receptor (EcR) isoforms (A, B1 and B2). This study revealed that the EcR/USP heterodimer displays isoform-specific capabilities. EcRB1 is normally induced with a form of USP that is missing its DNA-binding domain (DBD), although potentiation by juvenile hormone (JH) III is reduced. The EcRA and B2 isoforms, however, display almost no response to ecdysteroids with the DBD(-) USP. A mutation, K497E, in the shared ligand-binding domain of the EcR isoforms caused elevated EcRB2-specific affinity for a canonical ecdysone response element. The effects of directed modification and mutagenesis offer a strategy for developing hypotheses and considerations for studying in vivo function.
C1‐Inhibitor Reduces the Ischaemia–Reperfusion Injury of Skeletal Muscles in Mice after Aortic Cross‐Clamping (2002)

The data support a beneficial role for C1-INH in the treatment of ischaemia-reperfusion injuries of skeletal muscles.
Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery (2011)

Esophageal squamous cell carcinoma (ESCC) is among the top ten most frequent malignancies worldwide. In this study, our objective was to identify potential biomarkers for ESCC through a quantitative proteomic approach using the isobaric tags for relative and absolute quantitation (iTRAQ) approach. We compared the protein expression profiles of ESCC tumor tissues with the corresponding adjacent normal tissue from ten patients. LC-MS/MS analysis of strong cation exchange chromatography fractions was carried out on an Accurate Mass QTOF mass spectrometer, which led to the identification of 687 proteins. In all, 257 proteins were identified as differentially expressed in ESCC as compared to normal. We found several previously known protein biomarkers to be upregulated in ESCC including thrombospondin 1 (THBS1), periostin 1 (POSTN) and heat shock 70 kDa protein 9 (HSPA9) confirming the validity of our approach. In addition, several novel proteins that had not been reported previously were identified in our screen. These novel biomarker candidates included prosaposin (PSAP), plectin 1 (PLEC1) and protein disulfide isomerase A 4 (PDIA4) that were further validated to be overexpressed by immunohistochemical labeling using tissue microarrays. The success of our study shows that this mass spectrometric strategy can be applied to cancers in general to develop a panel of candidate biomarkers, which can then be validated by other techniques.
The cyclin K/Cdk12 complex (2012)

Comment on: Blazek D, et al. Genes Dev 2011; 25:2158–72
High-resolution 4-D imaging using fringe analysis (2010)

Real-time 3-D imaging, otherwise known as 4-D imaging, is becoming increasingly important in areas such as medical science, entertainment, homeland security, and manufacturing. Numerous 3-D imaging techniques have been developed, but only a few of them have the potential to achieve realtime. Of these few, fringe analysis based techniques stand out, having many advantages over the rest. This paper will explain the principles behind fringe analysis based techniques, and will provide experimental results from systems using these techniques.
Dual-Mode EPR Detects the Initial Intermediate in Photoassembly of the Photosystem II Mn Cluster:  The Influence of Amino Acid Residue 170 of the D1 Polypeptide on Mn Coordination (2000)

We report the first parallel polarization EPR signal from the Mn(III) ion formed by photooxidation of Mn(II) bound at the high affinity Mn-binding site of photosystem II (PSII). This species corresponds to the first photoactivation intermediate formed on the pathway to assembly of the water-splitting Mn cluster. The parallel mode EPR spectrum of the photooxidation product of 1.2/1 stoichiometry Mn(II)/Mn-depleted wild-type Synechocystis sp. PCC 6803 PSII particles consists of six well-resolved transitions split by a relatively small 55Mn hyperfine coupling (44 G). This spectral signature is absent in photooxidized Mn apoPSII complexes prepared from D1-Asp170Glu and D1-Asp170His mutants, providing direct spectral evidence for a role for this specific D1-Asp170 residue in the initial photoactivation chemistry. Temperature-dependence measurements and spectral simulations performed on the Mn(III) parallel mode EPR signal of the wild-type sample give an axial zero-field splitting value of D ≈ −2.5 cm-1 and a rhombic zero-field splitting value of |E| ≈ 0.269 cm-1. The negative D value for this d4 ion is indicative of either a 5B1g symmetry ground state of an octahedral Mn(III) geometry or a 5B1 symmetry ground state of a five-coordinate square-pyramidal Mn(III) geometry. The parallel mode Mn(III) EPR spectrum obtained from the wild-type photooxidized Mn apoPSII complex is contrasted with that obtained from the five-coordinate Mn(III) form of native Mn superoxide dismutase, which has a trigonal-bipyramidal geometry and a 5A1 symmetry ground state giving rise to a positive D value and a much larger 55Mn hyperfine coupling of 100 G. The D1-Asp170His mutant displays a parallel mode EPR spectrum similar to that observed in a Mn(III) model complex. The D1-Asp170Glu mutant shows no parallel mode spectrum, but in perpendicular mode it shows a broad feature near g = 5 which has spectral characteristics of an S = 3/2 Mn(IV) ion. This suggests that this mutant provides a binding site with a less positive Mn(III)/Mn(IV) reduction potential.
Surface free energy of poly(ethylene terephthalate) and nylon 6 films treated with low temperature plasma. (1987)

Poly (ethylene terephthalate) (PET) and nylon 6 films were treated with low temperature plasma in various gases, oxygen, nitrogen, hydrogen, helium, argon, methane, tetrafluoromethane, trifluoromethane, monochlorotrifluoromethane, and tetramethylsilane. The contact angles of various liquids of different surface tensions on the plasma-treated films were measured. The lowest surface tension γc (Zisman) and the highest surface tension γc (max) of the polymers were determined on the basis of the Zisman plots. Furthermore, the contributions of nonpolar dispersion, dipole, and hydrogen bonding forces to the surface tensions for the plasma-modified polymers were evaluated by the extended Fowkes equation. In addition, the plasma-treated samples were characterized by X-ray photoelectron spectroscopy (ESCA). The change in surface free energy of the plasma-treated films was correlated with their surface chemical compositions measured by ESCA.
Immersive VR for scientific visualization: a progress report (2000)

Immersive virtual reality (IVR) has the potential to be a powerful tool for the visualization of burgeoning scientific data sets and models. We sketch a research agenda for the hardware and software technology underlying IVR for scientific visualization. In contrast to Brooks' (1999) excellent survey which reported on the state of IVR and provided concrete examples of its production use, this article is somewhat speculative. It does not present solutions but rather a progress report, a hope, and a call to action, to help scientists cope with a major crisis that threatens to impede their progress.
Right Phrenic Nerve Injury Following Electrical Disconnection of the Right Superior Pulmonary Vein (2004)

This report describes a case of transient paresis of the right diaphragm following the transcatheter radiofrequency ablation for the electrical disconnection of pulmonary veins, which recovered completely during the observational period in a 61-year-old woman with paroxysmal atrial fibrillation. For electrical disconnection of pulmonary veins, careful preventive measures for phrenic nerve damage are required.
2002 Medicinal Chemistry Division Award Address:  Monoamine Transporters and Opioid Receptors. Targets for Addiction Therapy (2003)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXT2002 Medicinal Chemistry Division Award Address: Monoamine Transporters and Opioid Receptors. Targets for Addiction Therapy†F. Ivy CarrollView Author Information Chemistry and Life Sciences Group, Research Triangle Institute, P.O. Box 12194, Research Triangle Park, North Carolina 27709 Cite this: J. Med. Chem. 2003, 46, 10, 1775–1794Publication Date (Web):April 9, 2003Publication History Received24 February 2003Published online9 April 2003Published inissue 1 May 2003https://pubs.acs.org/doi/10.1021/jm030092dhttps://doi.org/10.1021/jm030092dreview-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views872Altmetric-Citations81LEARN 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 SUBJECTS:Amines,Antagonists,Ligands,Pharmaceuticals,Receptors Get e-Alerts
7-Oxabicyclo[2.2.1]heptyl carboxylic acids as thromboxane A2 antagonists: aza .omega.-chain analogs (1990)

A novel bicyclic prostaglandin analogue, [1S-[1 alpha, 2 alpha (Z), 3 alpha, 4 alpha]]-7-[3-[[[[(1- Oxoheptyl)amino]acetyl]amino]-methyl]-7-oxabicyclo[2.2.1]hept-2- yl]-5-heptenoic acid [-)-7) was found to be a potent and selective thromboxane A2 (TxA2) receptor antagonist. Unlike the related series of omega-chain allylic alcohols, amide 7 and its congeners were uniformly free of direct contractile activity in vitro (bovine coronary) and in vivo (anesthetized guinea pig). Amide 7 was effective in the inhibition of (a) arachidonic acid induced platelet aggregation of human platelet-rich plasma (I50 = 0.18 +/- 0.006 microM), (b) 11,9-epoxymethano-PGH2 induced platelet aggregation of human platelet-rich plasma (I50 = 0.24 microM), (c) 11,9-epoxymethano-PGH2 induced contraction of guinea pig trachea (Kb = 3.0 +/- 0.3 nM) or rat aorta (Kb = 8.8 +/- 1.1 nM), and (d) arachidonic acid induced bronchoconstriction in the anesthetized guinea pig (0.1-1.0 mg/kg iv). Amide 7 inhibited the binding of [5,6-3H2]-[1S- (1 alpha, 2 alpha (Z), 3 alpha, 4 alpha)]-7-[3-[[2-[(Phenyl- amino)carbonyl]hydrazino]methyl]-7-oxabicyclo[2.2.1]hept-2-yl]-5- heptenoic acid to human platelet membranes in a specific and saturable manner with a Kd = 49.6 +/- 1.4 nM.
Development of a model to demonstrate photosensitizer‐mediated viral inactivation in blood (1990)

A model has been developed to demonstrate the use of photodynamic treatment (PDT) to eradicate viral contaminants from donated blood and blood products. Whole blood, spiked with vesicular stomatitis virus (VSV), was treated with the photosensitizer benzoporphyrin derivative-monoacid ring A (BPD-MA). After light activation of BPD-MA, a neutral red dye uptake assay was carried out to determine virus inactivation. Various drug incubation times and light intensities were tested as well as red cell lysis and distribution of VSV in blood. At BPD-MA concentrations between 2 and 4 micrograms per mL in whole blood, up to 10(7) VSV were inactivated. Several photosensitizers were also tested with this model to determine their relative efficacy in viral inactivation.
URL diving (1998)

Perhaps the most important difference among search sites is how they are structured, both internally and externally. Sites such as Yahoo include a highly structured system of categories to help users drill down to the site they want. Others, such as AltaVista, accept only word-based searches with no categorical structure or browsing at all. There are also those that offer combinations of searching and browsing, with some variations to set them apart, such as ratings for some of the sites in their database, enabling searches among only prequalified sites. Finally, there are the so-called "metasearch" sites, which have no indexes of their own, but rather query, refilter, and compile results based on searches among multiple search engines. Perhaps the most important thing to understand is how search sites build and maintain their database indexes. There are two primary methods in use: registration and robot crawlers. Both have their own strengths and weaknesses, and consequently a place in every researcher's toolbox.
Estimation of near-surface shear-wave velocity by inversion of Rayleigh waves (1999)

Abstract The shear-wave (S-wave) velocity of near-surface materials (soil, rocks, pavement) and its effect on seismic-wave propagation are of fundamental interest in many groundwater, engineering, and environmental studies. Rayleigh-wave phase velocity of a layered-earth model is a function of frequency and four groups of earth properties: P-wave velocity, S-wave velocity, density, and thickness of layers. Analysis of the Jacobian matrix provides a measure of dispersion-curve sensitivity to earth properties. S-wave velocities are the dominant influence on a dispersion curve in a high-frequency range (&amp;gt;5 Hz) followed by layer thickness. An iterative solution technique to the weighted equation proved very effective in the high-frequency range when using the Levenberg-Marquardt and singular-value decomposition techniques. Convergence of the weighted solution is guaranteed through selection of the damping factor using the Levenberg-Marquardt method. Synthetic examples demonstrated calculation efficiency and stability of inverse procedures. We verify our method using borehole S-wave velocity measurements.
Sensory Neurons and Schwann Cells Respond to Oxidative Stress by Increasing Antioxidant Defense Mechanisms (2008)

Elevated blood glucose is a key initiator of mechanisms leading to diabetic neuropathy. Increases in glucose induce acute mitochondrial oxidative stress in dorsal root ganglion (DRG) neurons, the sensory neurons normally affected in diabetic neuropathy, whereas Schwann cells are largely unaffected. We propose that activation of an antioxidant response in DRG neurons would prevent glucose-induced injury. In this study, mild oxidative stress (1 microM H2O2) leads to the activation of the transcription factor Nrf2 and expression of antioxidant (phase II) enzymes. DRG neurons are thus protected from subsequent hyperglycemia-induced injury, as determined by activation of caspase 3 and the TUNEL assay. Schwann cells display high basal antioxidant enzyme expression and respond to hyperglycemia and mild oxidative stress via further increases in these enzymes. The botanical compounds resveratrol and sulforaphane activate the antioxidant response in DRG neurons. Other drugs that protect DRG neurons and block mitochondrial superoxide, identified in a compound screen, have differential ability to activate the antioxidant response. Multiple cellular targets exist for the prevention of hyperglycemic oxidative stress in DRG neurons, and these form the basis for new therapeutic strategies against diabetic neuropathy.