gebhart/patrepeval huggingface dataset:
Immunization with HIV Gag targeted to dendritic cells followed by recombinant New York vaccinia virus induces robust T-cell immunity in nonhuman primates (2011)

Protein vaccines, if rendered immunogenic, would facilitate vaccine development against HIV and other pathogens. We compared in nonhuman primates (NHPs) immune responses to HIV Gag p24 within 3G9 antibody to DEC205 ("DEC-HIV Gag p24"), an uptake receptor on dendritic cells, to nontargeted protein, with or without poly ICLC, a synthetic double stranded RNA, as adjuvant. Priming s.c. with 60 μg of both HIV Gag p24 vaccines elicited potent CD4(+) T cells secreting IL-2, IFN-γ, and TNF-α, which also proliferated. The responses increased with each of three immunizations and recognized multiple Gag peptides. DEC-HIV Gag p24 showed better cross-priming for CD8(+) T cells, whereas the avidity of anti-Gag antibodies was ∼10-fold higher with nontargeted Gag 24 protein. For both protein vaccines, poly ICLC was essential for T- and B-cell immunity. To determine whether adaptive responses could be further enhanced, animals were boosted with New York vaccinia virus (NYVAC)-HIV Gag/Pol/Nef. Gag-specific CD4(+) and CD8(+) T-cell responses increased markedly after priming with both protein vaccines and poly ICLC. These data reveal qualitative differences in antibody and T-cell responses to DEC-HIV Gag p24 and Gag p24 protein and show that prime boost with protein and adjuvant followed by NYVAC elicits potent cellular immunity.
Imaging Multiple Conductance States in an Alamethicin Pore (2011)

Alamethicin is the archetypal antimicrobial pore-forming peptide. Although the peptide has long been known to form pores of characteristic conductances in lipid membranes, the precise nature of these pores is not known. Simultaneous calcium-flux imaging and single-channel recording in a droplet interface bilayer allowed us to directly attribute multiple conductance states to a single point diffusing in the bilayer.
Activation of purified hepatoma RNA polymerase I by homologous protein kinase NII. (1981)

We have recently purified a cyclic nucleotide-independent, heparin-sensitive nuclear protein kinase (NII) from Morris hepatoma 3924A and demonstrated an apparent relationship of this kinase to the two subunits (Mr = 42,000 and 24,600) of RNA polymerase I. When homogeneous protein kinase NII was recombined with purified homologous RNA polymerase I containing limiting quantities of endogenous kinase, RNA synthesis was stimulated as much as 5-fold during a 90-min incubation. The enhanced RNA synthesis was due to an increase in the average RNA chain length; protein kinase did not alter the number of RNA molecules synthesized by the polymerase. Phosphorylation of RNA polymerase occurred at serine and threonine moieties. Unlike the NII kinase, purified homologous NI kinase did not phosphorylate RNA polymerase I and, as a result, did not alter transcription. These data indicate that 1) RNA polymerase I is activated by protein kinase NII, 2) endogenous protein kinase NII remaining with highly purified RNA polymerase I does not fully phosphorylate RNA polymerase I in vitro, and 3) protein kinase NII is capable of regulating RNA polymerase I activity by preventing premature termination of RNA chains.
Mapping Structures for Flash Memories: Techniques and Open Problems (2005)

Flash memory is a type of electrically erasable programmable read-only memory (EEPROM). Because flash memories are nonvolatile and relatively dense, they are now used to store files and other persistent objects in handheld computers, mobile phones, digital cameras, portable music players, and many other computer systems in which magnetic disks are inappropriate. Flash, like earlier EEPROM devices, suffers from two limitations. First, bits can only be cleared by erasing a large block of memory. Second, each block can only sustain a limited number of erasures, after which it can no longer reliably store data. Due to these limitations, sophisticated data structures and algorithms are required to effectively use flash memories. These algorithms and data structures support efficient not-in-place updates of data, reduce the number of erasures, and level the wear of the blocks in the device. This survey presents these algorithms and data structures as well as open theoretical problems that arise in this area.
Alternative promoter usage and tissue specific expression of the mouse somatostatin receptor 2 gene (1998)

We have cloned the 5' upstream regulatory region of the mouse somatostatin receptor 2 gene. Its genomic organization is novel among all somatostatin receptor genes. It contains two previously unrecognized exons, separated by introns larger than 25 kb, and three tissue and cell specific alternative promoters. The first promoter in front of exon 1 is active only in AtT-20 tumor cells. The second promoter, located 5' to exon 2, is used in brain, pituitary, adrenals, pancreas, NG 108-15 and AtT-20 cells. Furthermore, it contains putative DNA elements for regulation by glucocorticoids, estradiol and cAMP. A third promoter, located in exon 3, is additionally used in lung, kidney and spleen.
Resolution and some properties of enzymes involved in enantioselective transformation of 1,3-dichloro-2-propanol to (R)-3-chloro-1,2-propanediol by Corynebacterium sp. strain N-1074 (1992)

During the course of the transformation of 1,3-dichloro-2-propanol (DCP) into (R)-3-chloro-1,2-propanediol [(R)-MCP] with the cell extract of Corynebacterium sp. strain N-1074, epichlorohydrin (ECH) was transiently formed. The cell extract was fractionated into two DCP-dechlorinating activities (fractions Ia and Ib) and two ECH-hydrolyzing activities (fractions IIa and IIb) by TSKgel DEAE-5PW column chromatography. Fractions Ia and Ib catalyzed the interconversion of DCP to ECH, and fractions IIa and IIb catalyzed the transformation of ECH into MCP. Fractions Ia and IIa showed only low enantioselectivity for each reaction, whereas fractions Ib and IIb exhibited considerable enantioselectivity, yielding R-rich ECH and MCP, respectively. Enzymes Ia and Ib were isolated from fractions Ia and Ib, respectively. Enzyme Ia had a molecular mass of about 108 kDa and consisted of four subunits identical in molecular mass (about 28 kDa). Enzyme Ib was a protein of 115 kDa, composed of two different polypeptides (about 35 and 32 kDa). The specific activity of enzyme Ib for DCP was about 30-fold higher than that of enzyme Ia. Both enzymes catalyzed the transformation of several halohydrins into the corresponding epoxides with liberation of halides and its reverse reaction. Their substrate specificities and immunological properties differed from each other. Enzyme Ia seemed to be halohydrin hydrogen-halide-lyase which was already purified from Escherichia coli carrying a gene from Corynebacterium sp. strain N-1074.
Technology 1993 - Data communications (1993)

Trends and events during 1992 are reviewed. The pace quickened for standardization activities regarding ATM (asynchronous transfer mode) switching, the prime candidate for future networks. Tied in with the ATM activities, gigabit-per-second testbeds are sprouting in data communications research facilities. Internet continued to grow, with about 10000 networks and more than a million computers now connected and the computer population doubling every seven months. A competing technology, services based on low-orbiting satellites, gained a following.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Acid-sensitive Ionic Channel Subunit ASIC and the Mammalian Degenerin MDEG Form a Heteromultimeric H+-gated Na+ Channel with Novel Properties (1997)

Proton-gated cation channels are acid sensors that are present in both sensory neurons and in neurons of the central nervous system. One of these acid-sensing ion channels (ASIC) has been recently cloned. This paper shows that ASIC and the mammalian degenerin MDEG, which are colocalized in the same brain regions, can directly associate with each other. Immunoprecipitation of MDEG causes coprecipitation of ASIC. Moreover, coexpression of ASIC and MDEG subunits in Xenopus oocytes generates an amiloride-sensitive H+-gated Na+ channel with novel properties (different kinetics, ionic selectivity, and pH sensitivity). In addition, coexpression of MDEG with mutants of the ASIC subunit can create constitutively active channels that become completely nonselective for Na+ versus K+ and H+-gated channels that have a drastically altered pH sensitivity compared with MDEG. These data clearly show that ASIC and MDEG can form heteromultimeric assemblies with novel properties. Heteromultimeric assembly is probably used for creating a diversity of H+-gated cation channels acting as neuronal acid sensors in different pH ranges.
Registration of a SPOT image and a SAR image using multiresolution representation of a coastline (2002)

A novel method is presented for the registration of a SPOT satellite image against a Seasat synthetic aperture radar (SAR) image. An edge following technique is proposed. It is adapted to very noisy images such as SAR images. It is shown that, by the use of a multiresolution method, a directional graph can be constructed which gives a clearer definition of the equivalence between edge following and optimal path search on a graph. A hypothesis-testing approach, also based on a multiresolution method, is proposed to solve the registration problem. The hypotheses are drawn from scale space representations in order to maintain a low complexity. These hypotheses are then tested by a chamfer distance map. By the combination of scale space representation and the chamfer matching method, a very robust and fast registration results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A laboratory exercise introducing students to the Pourbaix for cobalt (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA laboratory exercise introducing students to the Pourbaix for cobaltDick Powell , Jim Cortez , and E. K. Mellon Cite this: J. Chem. Educ. 1987, 64, 2, 165Publication Date (Print):February 1, 1987Publication History Received3 August 2009Published online1 February 1987Published inissue 1 February 1987https://doi.org/10.1021/ed064p165RIGHTS & PERMISSIONSArticle Views1072Altmetric-Citations17LEARN 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 (2 MB) Get e-Alerts Get e-Alerts
PID control system analysis, design, and technology (2005)

Designing and tuning a proportional-integral-derivative (PID) controller appears to be conceptually intuitive, but can be hard in practice, if multiple (and often conflicting) objectives such as short transient and high stability are to be achieved. Usually, initial designs obtained by all means need to be adjusted repeatedly through computer simulations until the closed-loop system performs or compromises as desired. This stimulates the development of "intelligent" tools that can assist engineers to achieve the best overall PID control for the entire operating envelope. This development has further led to the incorporation of some advanced tuning algorithms into PID hardware modules. Corresponding to these developments, this paper presents a modern overview of functionalities and tuning methods in patents, software packages and commercial hardware modules. It is seen that many PID variants have been developed in order to improve transient performance, but standardising and modularising PID control are desired, although challenging. The inclusion of system identification and "intelligent" techniques in software based PID systems helps automate the entire design and tuning process to a useful degree. This should also assist future development of "plug-and-play" PID controllers that are widely applicable and can be set up easily and operate optimally for enhanced productivity, improved quality and reduced maintenance requirements.
Synthetic Lethality Exploitation by an Anti–Trop-2-SN-38 Antibody–Drug Conjugate, IMMU-132, Plus PARP Inhibitors in BRCA1/2 –wild-type Triple-Negative Breast Cancer (2017)

<b>Purpose:</b> Both PARP inhibitors (PARPi) and sacituzumab govitecan (IMMU-132) are currently under clinical evaluation in triple-negative breast cancer (TNBC). We sought to investigate the combined DNA-damaging effects of the topoisomerase I (Topo I)-inhibitory activity of IMMU-132 with PARPi disruption of DNA repair in TNBC.<b>Experimental Design:</b><i>In vitro</i>, human TNBC cell lines were incubated with IMMU-132 and various PARPi (olaparib, rucaparib, or talazoparib) to determine the effect on growth, double-stranded DNA (dsDNA) breaks, and cell-cycle arrest. Mice bearing <i>BRCA1/2</i>-mutated or -wild-type human TNBC tumor xenografts were treated with the combination of IMMU-132 and PARPi (olaparib or talazoparib). Study survival endpoint was tumor progression to >1.0 cm<sup>3</sup> and tolerability assessed by hematologic changes.<b>Results:</b> Combining IMMU-132 in TNBC with all three different PARPi results in synergistic growth inhibition, increased dsDNA breaks, and accumulation of cells in the S-phase of the cell cycle, regardless of <i>BRCA1/2</i> status. A combination of IMMU-132 plus olaparib or talazoparib produces significantly improved antitumor effects and delay in time-to-tumor progression compared with monotherapy in mice bearing <i>BRCA1/2</i>-mutated HCC1806 TNBC tumors. Furthermore, in mice bearing <i>BRCA1/2</i>-wild-type tumors (MDA-MB-468 or MDA-MB-231), the combination of IMMU-132 plus olaparib imparts a significant antitumor effect and survival benefit above that achieved with monotherapy. Most importantly, this combination was well tolerated, with no substantial changes in hematologic parameters.<b>Conclusions:</b> These data demonstrate the added benefit of combining Topo I inhibition mediated by IMMU-132 with synthetic lethality provided by PARPi in TNBC, regardless of <i>BRCA1/2</i> status, thus supporting the rationale for such a combination clinically. <i>Clin Cancer Res; 23(13); 3405-15. ©2017 AACR</i>.
Effect of amino acid substitutions in the heavy chain CDR3 of an autoantibody on its reactivity (1998)

In this study, we applied site-directed mutagenesis to the Fab fragment of a mouse IgM (IE12) that was previously shown to inhibit the binding of IgG to autoantigens by interacting with their variable regions. Its native structure was very similar to that of a polyreactive natural IgM (ppc15-30). Indeed, they both use the same light chain and the same VH, D and JH segments. However, the N regions differ and the D is translated in two different reading frames, giving different amino acid compositions of the heavy chain CDR3 (HCDR3). Site-directed mutagenesis modified the HCDR3 of IE12 compared to that of the natural antibody and the resulting effects on its reactivity were analyzed. Because the HCDR3 of IE12 is very rich in aliphatic residues, which are hydrophobic, we replaced them with the more hydrophilic residues of the HCDR3 of the polyreactive IgM. In addition, we evaluated the impact of the proline residues in the HCDR3 of IE12 on its activity, because they are known to restrict backbone flexibility. We found that a more hydrophilic HCDR3 conferred to the IE12 Fab a polyreactive profile. Prolines seem to play an important role in this context, because when they were replaced by glycines, the resulting Fab fragments were highly polyreactive. Our results suggest that, for polyreactivity, hydrophilicity and a certain plasticity of the HCDR3 seem to be necessary. Greater flexibility of the CDR, particularly the HCDR3, might be an important characteristic for polyreactive antibodies.
Optimization of mutual information for multiresolution image registration (2000)

We propose a new method for the intermodal registration of images using a criterion known as mutual information. Our main contribution is an optimizer that we specifically designed for this criterion. We show that this new optimizer is well adapted to a multiresolution approach because it typically converges in fewer criterion evaluations than other optimizers. We have built a multiresolution image pyramid, along with an interpolation process, an optimizer, and the criterion itself, around the unifying concept of spline-processing. This ensures coherence in the way we model data and yields good performance. We have tested our approach in a variety of experimental conditions and report excellent results. We claim an accuracy of about a hundredth of a pixel under ideal conditions. We are also robust since the accuracy is still about a tenth of a pixel under very noisy conditions. In addition, a blind evaluation of our results compares very favorably to the work of several other researchers.
Expression of HLA-DR4 and human CD4 transgenes in mice determines the variable region beta-chain T-cell repertoire and mediates an HLA-DR-restricted immune response. (1994)

Inherited susceptibility to rheumatoid arthritis is associated with genes encoding the human major histocompatibility complex class II molecule HLA-DR4. To study the immune function of HLA-DR4 and attempt to generate a murine model of rheumatoid arthritis we have produced triple transgenic mice expressing HLA-DRA*0101, -DRB1*0401, and human CD4. The expression of the HLA transgenes is driven by the promoter of the murine major histocompatibility complex class II I-E alpha gene and was found on murine cells that normally display major histocompatibility complex class II molecules. The expression of the human CD4 transgene is driven by the murine CD3 delta-promoter, and therefore its gene product was found on cells that express murine CD3. In contrast to other HLA-DR and HLA-DQ transgenic mouse lines, the transgenes are functional in our mice. In H-2 I-E-negative transgenic mice, T cells expressing variable region beta chain (V beta) 3, 5, 6, 7, 9, 11, 12, or 13 were either absent or significantly reduced, in contrast to H-2 I-E-negative nontransgenic littermates. In addition, the peptide antigen influenza A virus hemagglutinin 307-319, which binds to the HLA-DRA*0101/-DRB1*0401 heterodimer with high affinity and induces an HLA-DR-restricted and CD4+ T-cell response in humans, also induced a T-cell response in the triple transgenic mice but not in nontransgenic littermates. Thus, these transgenic mice should permit extensive testing of the antigen-presentation capabilities of the HLA-DRA*0101/-DRB1*0401 molecule.
Mechanism of nitric oxide-dependent killing of Mycobacterium bovis BCG in human alveolar macrophages (1997)

We demonstrated that products of the L-arginine-dependent pathway of human alveolar macrophages (AM) effectively kill the Mycobacterium bovis bacillus Calmette-Guérin (BCG) in vitro. The formation of products was triggered by inoculation with BCG itself. Many reports have shown that activated rodent AM could produce an amount of nitric oxide (NO) sufficient to suppress the growth of mycobacteria. However, there have been no definitive results as to whether human AM might have the NO-dependent mechanism for the killing of mycobacteria. Therefore, we have undertaken some experiments to answer this question. Immunofluorescence assays showed an increased production of inducible nitric oxide synthase (iNOS) and peroxynitrite in BCG-inoculated AM from patients with pulmonary fibrosis. Reverse transcriptase-PCR also revealed the higher expression of iNOS-coding mRNA. Colony assays demonstrated that these human AM effectively killed BCG in their cytoplasm. However, treatment of AM with N(G)-monomethyl-L-arginine monoacetate resulted in markedly reduced killing activity. These results clearly show that BCG-induced NO and its reactive product with the oxygen radical peroxynitrite could play an important role in the killing of BCG in human AM.
Application of solid dispersions with enteric coating agents to overcome some pharmaceutical problems. (1986)

A solid dispersion technique with enteric coating agents was applied to two drugs which present some pharmaceutical problems. The first drug, digoxin, is poorly water-soluble and chemically unstable in an acidic medium. The solid dispersions suppressed the dissolution rate of the drug in JP X 1st fluid (JP disintegration medium, pH 1.2), and improved the chemical stability.In JP X 2nd fluid (JP disintegration medium, pH 6.8), the solid dispersions showed rapid dissolution and supersaturation. It was concluded that this technique can provide an effective dosage form of digoxin for gastrointestinal absorption. The second drug, dipyridamole, is a poorly water-soluble organic base. The solid dispersion technique was applied to prepare a delayed absorption dosage form with good bioavailability. The solid dispersions showed suppressed a dissolution in an acidic medium, and gave supersaturation in a neutral or alkaline medium. Oral administration of this dosage form resulted in delayed absorption with good bioavailability.
Atom Transfer Radical Polymerization (ATRP) and Addition (ATRA) and Applications (2012)

Abstract Fundamentals of transition‐metal‐catalyzed atom transfer radical polymerization (ATRP) and mechanistically similar atom transfer radical addition (ATRA) are discussed. Both processes utilize transition‐metal complexes as halogen atom transfer agents. ATRP enables the synthesis of polymeric materials with well‐controlled molecular weight, molecular weight distribution, composition, molecular architecture, and chain‐end functionality. ATRA, on the other hand, is particularly suitable for the synthesis of small and highly functional organic molecules. Basic phenomenology, components (alkyl halide, monomer, solvent, and catalyst), as well as current and forthcoming applications are reviewed.
Properties of a novel noncascaded type, easy-to-design, ripple-free optical bandpass filter (1999)

The chief principle and properties of a novel noncascaded type optical bandpass filter with three unique general characteristics are presented. This device is based on a combination of a Michelson interferometer and a Gires-Tournois resonator (GTR). First, the filter has square-like frequency response with zero ripple, wide flat-top (0.74/spl times/bandwidth), unity contrast, sharp steepness, and infinite rejection ratio when GTR front surface mirror reflectance /spl rho/ is equal to one-third. Second, this filter possesses variable bandwidth and center wavelength tunability features with simple control mechanism and nanosecond temporal response potential. Third, the desired features of the filter can be synthesized easily by mere inspection since only three parameters are required, and their expressions are given in simple analytic forms. Numerical results showing these features are presented and other characteristics are briefly discussed.