gebhart/patrepeval huggingface dataset:
Hydrothermal catalytic production of fuels and chemicals from aquatic biomass (2012)

Abstract One of the promising avenues for biomass processing is the use of water as a reaction medium for wet or aquatic biomass. This review focuses on the hydrothermal catalytic production of fuels and chemicals from aquatic biomass. Two different regimes for conversion of aquatic biomass in hydrothermal conditions are discussed in detail. The first is hydrothermal liquefaction, and the second is hydrothermal gasification. The goals of these processes are to produce liquid‐fuel‐range hydrocarbons and methane or hydrogen, respectively. The catalytic upgrading of biocrude resulting from noncatalytic liquefaction and the stability and degradation of catalysts in high temperature water are also discussed. The review concludes with a brief discussion of the outlook for and opportunities within the field of hydrothermal catalytic valorization of biomass. Copyright © 2012 Society of Chemical Industry
Programmatic gold: targeted and scalable quality assurance in crowdsourcing (2011)

Crowdsourcing is an effective tool for scalable data annota-tion in both research and enterprise contexts. Due to crowd-sourcing’s open participation model, quality assurance is crit-ical to the success of any project. Present methods rely on EM-style post-processing or manual annotation of large gold standard sets. In this paper we present an automated quality assurance process that is inexpensive and scalable. Our novel process relies on programmatic gold creation to provide tar-geted training feedback to workers and to prevent common scamming scenarios. We find that it decreases the amount of manual work required to manage crowdsourced labor while improving the overall quality of the results. 1
Physical mechanisms and rates of particle capture by suspension-feeders (1991)

Models of particle encounter efficiency borrowed from aerosol fil- tration theory have revolutionised ideas about mechanisms of suspension-feeding (a form of hydrosol filtration), although they continue to be under-utilised in generating predictions concerning feeding ecology and morphological evolution and in guiding quantitative experimentation . As a complementary tool we model encounter rate, demonstrated with parameterisations ofthe same particle-encounter mechanisms . The rate models include specific encounter geometry, absent from the prevalent efficiency indices, which is used to refine estimates of the absolute and relative effectiveness of the various encounter mechanisms . Using rate (as opposed to effi- ciency and in accord with optimal foraging theory) as the dependent variable yields very different predictions for optimisation schemes . For example, a larger collector radius reduces encounter efficiency for most mechanisms, but it either increases or leaves unaffected encounter rate . Similarly, an increase in advection velocity often reduces encounter efficiency, but it increases encounter rate for most mechanisms
Measurement of transient cDNA expression in mammalian cells using flow cytometric cell analysis and sorting (1991)

Generalized methods for quantitative and sensitive measurement of transient cDNA expression in mammalian cells using flow cytometry (FCM) are described. The techniques are applicable to a wide variety of cDNAs encoding intracellular or cell surface protein products through the use of immunofluorescence- or nonimmunofluorescence-based detection methods. The methods illustrated have been optimized for sensitive detection of transfectants and efficient recovery of the encoding plasmids from the sorted cells. Expression levels and heterogeneities were compared using four methods of DNA transfer in addition to description of a novel method to optimize single copy transfer probabilities by multiparameter analysis. The overall sensitivities are compared by reconstruction and molecular cloning experiments to other methods of selection, such as immunoselection by panning. Through the measurement of multiple heterologous products per cell, or the measurement of multiple epitopes or binding sites per heterologous protein, expression levels on a single cell basis can be measured and correlated with other endpoints for various purposes. The ability to detect and recover rare clones based on a number of single and multiparameter selection criteria should significantly extend the use of transient mammalian cDNA expression methods for applications involving novel FCM-based reporter cDNA assays and for cloning certain rare surface-bound or secreted proteins using FCM.
A Live Recombinant Avirulent Oral Salmonella Vaccine Expressing Pneumococcal Surface Protein A Induces Protective Responses against Streptococcus pneumoniae (1998)

A live oral recombinant Salmonella vaccine strain expressing pneumococcal surface protein A (PspA) was developed. The strain was attenuated with Deltacya Deltacrp mutations. Stable expression of PspA was achieved by the use of the balanced-lethal vector-host system, which employs an asd deletion in the host chromosome to impose an obligate requirement for diaminopimelic acid. The chromosomal Deltaasd mutation was complemented by a plasmid vector possessing the asd+ gene. A portion of the pspA gene from Streptococcus pneumoniae Rx1 was cloned onto a multicopy Asd+ vector. After oral immunization, the recombinant Salmonella-PspA vaccine strain colonized the Peyer's patches, spleens, and livers of BALB/cByJ and CBA/N mice and stimulated humoral and mucosal antibody responses. Oral immunization of outbred New Zealand White rabbits with the recombinant Salmonella strain induced significant anti-PspA immunoglobulin G titers in serum and vaginal secretions. Polyclonal sera from orally immunized mice detected PspA on the S. pneumoniae cell surface as revealed by immunofluorescence. Oral immunization of BALB/cJ mice with the PspA-producing Salmonella strain elicited antibody to PspA and resistance to challenge by the mouse-virulent human clinical isolate S. pneumoniae WU2. Immune sera from orally immunized mice conferred passive protection against otherwise lethal intraperitoneal or intravascular challenge with strain WU2.
A cis-acting element from the Epstein-Barr viral genome that permits stable replication of recombinant plasmids in latently infected cells. (1984)

The Epstein-Barr viral (EBV) genome of approximately equal to 170 kilobase pairs (kbp) is maintained as a plasmid in human B lymphoblasts transformed by the virus. We have identified a cis-acting element within 1.8 kbp of the viral genome that allows recombinant plasmids carrying it to be selected at high frequency and maintained as plasmids in cells latently infected by EBV. This functional element(s) requires a segment of DNA at least 800 bp and at most 1800 bp long, which contains a family of 30-bp tandem repeats at one end. Since this region confers efficient stable replication only to plasmids transfected into cells containing EBV genomes, its function probably requires trans-acting products encoded elsewhere in the viral genome.
Antibacterial Peptide Protocols (1997)

As this book. Antibacterial Peptide Protocols, will attest, my enthusi asm for the field of antibacterial peptides is based on a conviction (and I am unashamed to say, prejudice) that these substances
Research on the Failure of Fiber Reinforced aluminum-based Wires for Conductor (2008)

This paper deals with the morphology and failure-resistance of fiber reinforced aluminum wire used for conductor. The stress-strain relationship of test materials was analyzed. The results show that this composite wire has an excellent failure-resistant performance.
Covalent catalysis in nucleotidyl transfer reactions: essential motifs in Saccharomyces cerevisiae RNA capping enzyme are conserved in Schizosaccharomyces pombe and viral capping enzymes and among polynucleotide ligases. (1994)

Formation of the 5' cap structure of eukaryotic mRNAs occurs via transfer of GMP from GTP to the 5' terminus of the primary transcript. RNA guanylyltransferase, the enzyme that catalyzes this reaction, has been isolated from many viral and cellular sources. Though differing in molecular weight and subunit structure, the various guanylyltransferases employ a common catalytic mechanism involving a covalent enzyme-(Lys-GMP) intermediate. Saccharomyces cerevisiae CEG1 is the sole example of a cellular capping enzyme gene. In this report, we describe the identification and characterization of the PCE1 gene encoding the capping enzyme from Schizosaccharomyces pombe. PCE1 was isolated from a cDNA library by functional complementation in Sa. cerevisiae. Induced expression of PCE1 in bacteria and in yeast confirmed that the 47-kDa Sc. pombe protein was enzymatically active. The amino acid sequence of PCE1 is 38% identical (152 of 402 residues) to the 52-kDa capping enzyme from Sa. cerevisiae. Comparison of the two cellular capping enzymes with guanylyltransferases encoded by DNA viruses revealed local sequence similarity at the enzyme's active site and at four additional collinear motifs. Mutational analysis of yeast CEG1 demonstrated that four of the five conserved motifs are essential for capping enzyme function in vivo. Remarkably, the same motifs are conserved in the polynucleotide ligase family of enzymes that employ an enzyme-(Lys-AMP) intermediate. These findings illuminate a shared structural basis for covalent catalysis in nucleotidyl transfer and suggest a common evolutionary origin for capping enzymes and ligases.
Analysis of Frequency Response Characteristics of Polymer Ultrasonic Transducers (1988)

Piezoelectric polymers have large dielectric and mechanical internal losses. In this study, we introduced internal losses into Mason's equivalent circuit, and analyzed the effects of these losses on the transducer response, mainly in the frequency domain. To prove the validity of the theoretical analysis, we fabricated polymer transducers of several backing load types which are effective for practical use, using vinylidene fluoride and trifluoroethylene copolymer films, and evaluated their frequency and impulse responses. The experimental results are in good agreement with the theoretical prediction. We conclude that a consideration of the internal losses is essential for the proper design and correct evaluation of polymer transducers.
Efficient Reformulation of Solid-Phase Diffusion in Physics-Based Lithium-Ion Battery Models (2010)

Lithium-ion batteries are typically modeled using porous electrode theory coupled with various transport and reaction mechanisms with an appropriate discretization or approximation for the solid phase. One of the major difficulties in simulating Li-ion battery models is the need for simulating solid-phase diffusion in a second dimension . It increases the complexity of the model as well as the computation time/cost to a great extent. Traditional approach toward solid-phase diffusion leads to more difficulties, with the use of emerging cathode materials, which involve phase changes and thus moving boundaries. A computationally efficient representation for solid-phase diffusion is discussed in this paper. The operating condition has a significant effect on the validity, accuracy, and efficiency of various approximations for the solid-phase diffusion. This paper compares approaches available today for solid-phase reformulation and provides two efficient forms for constant and varying diffusivities in the solid phase. This paper introduces an efficient method of an eigenfunction based Galerkin collocation and a mixed order finite difference method for approximating/representing solid-phase concentration variations within the active materials of porous electrodes for a pseudo-two-dimensional model for lithium-ion batteries.
Sound rendering (1992)

article Free Access Share on Sound rendering Authors: Tapio Takala Helsinki University of Technology, 02150 Espoo, Finland Helsinki University of Technology, 02150 Espoo, FinlandView Profile , James Hahn The George Washington University, Washington, DC 20052 The George Washington University, Washington, DC 20052View Profile Authors Info & Claims ACM SIGGRAPH Computer GraphicsVolume 26Issue 2July 1992 pp 211–220https://doi.org/10.1145/142920.134063Published:01 July 1992Publication History 126citation2,132DownloadsMetricsTotal Citations126Total Downloads2,132Last 12 Months140Last 6 weeks23 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Molecular Control of Immune/Inflammatory Responses: Interactions Between Nuclear Factor-κB and Steroid Receptor-Signaling Pathways (1999)

I. Introduction II. Nuclear Factor-κB (NF-κB) A. Introduction B. NF-κB is a dimeric transcription factor C. The regulatory subunit IκB is an inhibitor of NF-κB D. Activation and function of NF-κB E. The transcription factor NF-κB interacts with multiple transcription factors and transcriptional co-factors F. Transgenic animals suggest a complex role for NF-κB family members in immunity and development III. Steroid Hormones/Receptors: Glucocorticoids and the Glucocorticoid Receptor (GR) A. General background B. Glucocorticoid mechanism of action: the GR C. Glucocorticoid physiology D. GR/NF-κB interactions E. GR interacts with other transcription factors and transcriptional cofactors IV. NF-κB and GR Antagonism: Physiological Significance? V. Interactions Between NF-κB and Other Steroid Hormone Receptors A. Androgen receptor (AR) B. Estrogen receptor (ER) C. Progesterone receptor (PR) VI. Summary/Conclusions
Acquirement of Rituximab Resistance in Lymphoma Cell Lines Is Associated with Both GlobalCD20Gene and Protein Down-Regulation Regulated at the Pretranscriptional and Posttranscriptional Levels (2008)

Acquirement of resistance to rituximab has been observed in lymphoma patients. To define mechanisms associated with rituximab resistance, we developed various rituximab-resistant cell lines (RRCL) and studied changes in CD20 expression/structure, lipid raft domain (LRD) reorganization, calcium mobilization, antibody-dependent cellular cytotoxicity, and complement-mediated cytotoxicity (CMC) between parental and RRCL. Significant changes in surface CD20 antigen expression were shown in RRCL. Decreased calcium mobilization and redistribution of CD20 into LRD were found in RRCL. Western blotting identified a unique 35 kDa protein band in RRCL, which was not seen in parental cells and was secondary to an increase in surface and cytoplasmic expression of IgM light chains. CD20 gene expression was decreased in RRCL. In vitro exposure to PS341 increased CD20 expression in RRCL and minimally improved the sensitivity to rituximab-associated CMC. Our data strongly suggest that the acquisition of rituximab resistance is associated with global gene and protein down-regulation of the CD20 antigen affecting LRD organization and downstream signaling. CD20 expression seems to be regulated at the pretranscriptional and posttranscriptional levels. Proteasome inhibition partially reversed rituximab resistance, suggesting the existence of additional mediators of rituximab resistance. Future research is geared to identify drugs and/or biological agents that are effective against RRCL.
Benzothiadiazine Dioxide Human Cytomegalovirus Inhibitors: Synthesis and Antiviral Evaluation of Main Heterocycle Modified Derivatives (2003)

The benzothiadiazine dioxide derivatives are potent non-nucleoside human cytomegalovirus (HCMV) inhibitors. As part of our comprehensive structure-activity relationship (SAR) study of these compounds, we have now proposed structural modifications on the heterocyclic moiety both on the number and the nature of the fused heterocycle and on the kind of heteroatoms present on it. Synthesis of these new compounds (benzyl derivatives of thiadiazines, thienothiadiazines, benzothienothiadiazines and quinazolines) and the antiviral evaluation against HCMV has been performed. SAR investigation on this class of compounds has defined the structural requirements for potency and toxicity. They have revealed two important clues: i) a fused ring to the thiadiazine framework is necessary to maintain the anti-HCMV action, and ii) the sulfamido moiety in the main heterocycle is crucial to avoid cytotoxicity.
Molecular Cloning and Characterization of RGC-32, a Novel Gene Induced by Complement Activation in Oligodendrocytes (1998)

Sublytic complement activation on oligodendrocytes (OLG) down-regulates expression of myelin genes and induces cell cycle in culture. Differential display (DD) was used to search for new genes whose expression is altered in response to complement and that may be involved in cell cycle activation. DD bands showing either increased or decreased mRNA expression in response to complement were identified and designated Response Genes to Complement (RGC) 1-32. RGC-1 is identical with heat shock protein 105, RGC-2 with poly(ADP-ribose) polymerase, and RGC-10 with IP-10. A new gene, RGC-32, that encodes a protein of 137 amino acids was cloned. RGC-32 has no homology with other known proteins, and contains no motif that would indicate its function. In OLG, the mRNA expression was increased by complement activation and by terminal complement complex assembly. RGC-32 protein was localized in the cytoplasm and co-immunoprecipitated with cdc2 kinase. Overexpression of RGC-32 increased DNA synthesis in OLGxC6 glioma cell hybrids. These results suggest that RGC-32 may play a role in cell cycle activation.
Histopathological observations in the canine prostate treated by local microwave hyperthermia (1986)

A large series of repeated experiments were performed applying localized microwave hyperthermia to the prostate in dogs using a new water-cooled skirt-type antenna [1], operating at 915 MHz, as part of a new hyperthermia apparatus being developed for the treatment of the prostate in humans. The prostate gland of 20 male dogs was heated repeatedly under general anesthesia, at temperatures between 40 degrees C and 47 degrees C, and for different lengths of time up to 10 h. The prostate and other tissues were evaluated histopathologically following treatments. Invariably, all treatments by hyperthermia of the prostate caused a mononuclear inflammatory infiltration in the interstitium and polymorphonuclear infiltration in the glandular elements. Permanent tissue damage was found to be time-and temperature-dependent. Heating at 42.5 degrees C (+/- 0.5 degrees 5C) for up to 1.5 h was found to be harmless and could be safely repeated with our equipment. This study was part of a preclinical evaluation of a new antenna and apparatus.
Functional role of matrix metalloproteinases (MMPs) in mammary epithelial cell development (2001)

The extracellular matrix (ECM) is an important regulator of mammary epithelial cell (MEC) function and is remodeled by matrix metalloproteinases (MMPs). To investigate the significance and regulation of MMP activity in normal MEC, we utilized a primary culture model in which rat MEC were grown three dimensionally within a reconstituted basement membrane (RBM) in defined serum-free medium. Zymograms of culture medium demonstrated that five major gelatinases of 97, 80, 74, 69, and 65 kDa were secreted by MEC and were distinct from gelatinases of RBM origin. Based on molecular weight, p-aminophenylmercuric acid activation, immunoblotting with MMP-specific antibodies, inhibition by EDTA, a peptide containing the prodomain sequence of MMP (TMRKPRCGNPDVAN) and two synthetic MMP inhibitors (BB-94 and CGS 27023A), these were classified as inactive and active forms of MMP-9 and MMP-2. The maximal MMP activities occurred when MEC were in a rapid proliferation and branching phase and declined after they underwent functional differentiation. Known regulators of MEC growth and differentiation were evaluated for their ability to modulate gelatinase activity in primary culture. Secretion of one or both MMPs was inhibited by EGF, TGFalpha, prolactin, and hydrocortisone and stimulated by progesterone. Furthermore, the functional significance of MMPs was demonstrated since three MMP inhibitors blocked branching morphogenesis elicited by the absence of hydrocortisone. Additionally, two synthetic MMP inhibitors not only inhibited epithelial cell growth but also inhibited normal alveolar development of the MEC. Finally, these drugs were found to enhance MMP secretion from MEC, although the activity of the secreted MMPs was inhibited as long as the drug was present.
The Design and Synthesis of Water-Soluble Analogues of CB30865, a Quinazolin-4-one-Based Antitumor Agent (2002)

4-[N-[7-Bromo-2-methyl-4-oxo-3,4-dihydroquinazolin-6-ylmethyl]-N-(prop-2-ynyl)amino]-N-(3-pyridylmethyl)benzamide (CB30865) is a quinazolin-4-one antitumor agent whose high growth-inhibitory activity (W1L2 IC(50) = 2.8 +/- 0.50 nM) is believed to have a folate-independent locus of action. In addition, CB30865 represents a class of compounds with unique biochemical characteristics such as a delayed, non-phase specific, cell-cycle arrest. The low aqueous solubility of CB30865 prompted a search for more water-soluble analogues for in vivo evaluation of this class of compounds. It was thought that aqueous solubility could be increased by the introduction of amino functionalities at the 2-position of the quinazolin-4-one ring. A variety of compounds (5a-j, 31a-c, 32, and 33) were synthesized in a linear fashion starting from 3-chloro-4-methylaniline. Most of these compounds (e.g., 5a, 5b, 5g) were significantly more water-soluble than CB30865 (636 microM for 5a at pH 6 and 992 microM for 5g at pH 6). In addition, some of them were up to 6-fold more cytotoxic than CB30865 (e.g., for 5a, W1L2 IC(50) = 0.49 +/- 0.24 nM) and retained its novel biochemical characteristics.
A New Stent for the Treatment of Urethral Strictures (1989)

We describe a new urethral stent which was implanted into 12 patients with urethral strictures. The stent is woven in the form of a tubular mesh from fine stainless steel wire and is self-expanding when released from its small diameter delivery catheter. All patients have been treated successfully, with a good calibre urethra visible on urethrography and direct endoscopy and with improved urine flow rates. The mean follow-up of these patients was 7 months (range 2-13). Urethroscopy demonstrated complete epithelial covering of the implant in 4 to 6 months. Although the follow-up period was short, it seems that this simple technique may offer a lasting treatment for many urethral strictures. A longer follow-up will be necessary to exclude late complications.
CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification (2012)

High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method for overcoming this limitation by barcoding and pooling samples before linearly amplifying mRNA with the use of one round of in vitro transcription. We show that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method. We demonstrate the power of this method by studying early C. elegans embryonic development at single-cell resolution. Differential distribution of transcripts between sister cells is seen as early as the two-cell stage embryo, and zygotic expression in the somatic cell lineages is enriched for transcription factors. The robust transcriptome quantifications enabled by CEL-Seq will be useful for transcriptomic analyses of complex tissues containing populations of diverse cell types.