gebhart/patrepeval huggingface dataset:
Palladium-catalyzed Reaction of 3-Bromoindole Derivative with Allyl Esters in the Presence fo Hexa-n-butyldistannane (1990)

The palladium-catalyzed cross-coupling reaction of ethyl 3-bromo-1-tosyl-indole-2-carboxylate (9) with a variety of substituted allylic acetates or carbonates (10) in the presence of hexa-n-butyldistannane (6) gave-3-allylated indoles (11) in high yields
Shopping models (1997)

In a digital library, there are many diierent interaction models between customers and information providers or merchants. Subscriptions, sessions, pay-per-view, shareware, and pre-paid vouchers are different models that each have different properties. A single merchant may use several of them. Yet if a merchant wants to support multiple models, there is a substantial amount of work to implement each one. In this paper, we formalize the shopping models which represent these different modes of consumer to merchant interaction. In addition to developing the overall architecture, we define the application program interfaces (API) to interact with the models. We show how a small number of primitives can be used to construct a wide range of shopping models that a digital library can support, and provide examples of the shopping models in operation, demonstrating their fle.xibiity. Two models have been implemented as part of the Stanford Digital Library Project, to begin validating re-usability of key architectural components.
Employing Usability Engineering in the Development of Office Products (1988)

Usability engineering is the process whereby the usability of a product is specified quantitatively, and in advance. Then, as the product is built, testing takes place to see whether the planned-for levels of usability have been achieved. This paper describes the way that usability engineering has been implemented by a large engineering group building office software systems. The methods employed are described, and the measures that are taken. By means of two hypothetical product scenarios, it is demonstrated how usability testing is performed and the success that is achieved in feeding back early information to the software engineers. This feedback results in the improvement of the usability of the developing product. The paper ends with some guidelines for successful incorporation of usability engineering into the product development cycle.
Biodistribution of gadolinium‐based contrast agents, including gadolinium deposition (2009)

The biodistribution of approved gadolinium (Gd)-based contrast agents (GBCAs) is reviewed. After intravenous injection GBCAs distribute in the blood and the extracellular space and transiently through the excretory organs. Preclinical animal studies and the available clinical literature indicate that all these compounds are excreted intact. Elimination tends to be rapid and, for the most part, complete. In renally insufficient patients the plasma elimination half-life increases substantially from hours to days depending on renal function. In patients with impaired renal function and nephrogenic systemic fibrosis (NSF), the agents gadodiamide, gadoversetamide, and gadopentetate dimeglumine have been shown to result in Gd deposition in the skin and internal organs. In these cases, it is likely that the Gd is no longer present as the GBCA, but this has still not been definitively shown. In preclinical models very small amounts of Gd are retained in the bone and liver, and the amount retained correlates with the kinetic and thermodynamic stability of the GBCA with respect to Gd release in vitro. The pattern of residual Gd deposition in NSF subjects may be different than that observed in preclinical rodent models. GBCAs are designed to be used via intravenous administration. Altering the route of administration and/or the formulation of the GBCA can dramatically alter the biodistribution of the GBCA and can increase the likelihood of Gd deposition. J. Magn. Reson. Imaging 2009;30:1259-1267. (c) 2009 Wiley-Liss, Inc.
Head and Neck Cancer (1993)

Head and neck cancer was last reviewed in the Journal in 19831. At that time, there was promising new information on a possible role for chemotherapy1,2. During the past decade, chemotherapy has undergone further investigation and important clinical advances have been made in chemoprevention, organ preservation, and the simultaneous use of chemotherapy and radiation. In this review, we shall discuss the diagnosis of and standard therapy for head and neck cancer, as well as the status of recent basic and clinical investigations.EpidemiologyHead and neck cancer, as defined here, includes the common squamous-cell carcinomas of the . . .
Structure function studies on phytochrome. Identification of light-induced conformational changes in 124-kDa Avena phytochrome in vitro. (1985)

Light-mediated conformational changes in highly purified 124-kDa phytochrome preparations from etiolated oat seedlings have been identified by steric exclusion high performance liquid chromatography and limited proteolytic studies. Steric exclusion high performance liquid chromatography studies of oat and rye phytochromes show photoreversible changes in retention times, with the red absorbing form of phytochrome (Pr form) eluting later than the far red absorbing form of phytochrome produced by saturating red light illumination of Pr (Pfr form) in a variety of different mobile phase buffers. Molecular mass calibration with globular protein standards in Tris-glycol buffers provides estimates of 318-349 and 363-366 kDa for the molecular sizes of the Pr and Pfr forms, respectively. These analyses support earlier studies that phytochrome is a nonglobular homodimer of 124-kDa subunits in vitro. Limited proteolytic dissection of phytochrome in nondenaturing buffers with seven different endoproteases provides evidence for two "operational" domains within the 124-kDa subunit with molecular mass values of 69-72 and 52-55 kDa. The larger 69-72-kDa domain contains the site for the chromophore attachment as shown by gel electrophoresis derived enzyme-linked immunosorbent assay utilizing site-directed rabbit antiserum to a synthetic undecapeptide which is homologous with the chromophore binding site on oat phytochrome. This chromophore domain exhibits a compact structure, resistant to further proteolysis except near its N terminus. By contrast, the 52-55-kDa nonchromophore domain contains multiple sites for further proteolytic cleavage as revealed by rapid cleavage to smaller polypeptide fragments. Detailed kinetic analyses of the limited proteolytic cleavage of phytochrome with four endoproteases, subtilisin BPN', thermolysin, trypsin, and clostripain, has mapped specific regions within the 124-kDa subunit that participate in light-induced conformational changes. These include a 4-10-kDa region near the N terminus of the chromophore binding domain and at least two regions within the nonchromophore domain. A comprehensive peptide map of the oat phytochrome subunit is presented, which incorporates the results of these proteolytic studies with the recent, yet unpublished sequence analyses of Avena phytochrome cDNA clones which show the N-terminal localization of the chromophore binding site (Hershey, H. P., Colbert, J. T., Lissemore, J. L., Barker, R. F., and Quail, P. H. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 2332-2336).
Synthetic peptide vaccine development: measurement of polyclonal antibody affinity and cross‐reactivity using a new peptide capture and release system for surface plasmon resonance spectroscopy (2004)

A method has been developed for measurement of antibody affinity and cross-reactivity by surface plasmon resonance spectroscopy using the EK-coil heterodimeric coiled-coil peptide capture system. This system allows for reversible capture of synthetic peptide ligands on a biosensor chip surface, with the advantage that multiple antibody-antigen interactions can be analyzed using a single biosensor chip. This method has proven useful in the development of a synthetic peptide anti-Pseudomonas aeruginosa (PA) vaccine. Synthetic peptide ligands corresponding to the receptor binding domains of pilin from four strains of PA were conjugated to the E-coil strand of the heterodimeric coiled-coil domain and individually captured on the biosensor chip through dimerization with the immobilized K-coil strand. Polyclonal rabbit IgG raised against pilin epitopes was injected over the sensor chip surface for kinetic analysis of the antigen-antibody interaction. The kinetic rate constants, k(on) and k(off), and equilibrium association and dissociation constants, KA and KD, were calculated. Antibody affinities ranged from 1.14 x 10(-9) to 1.60 x 10(-5) M. The results suggest that the carrier protein and adjuvant used during immunization make a dramatic difference in antibody affinity and cross-reactivity. Antibodies raised against the PA strain K pilin epitope conjugated to keyhole limpet haemocyanin using Freund's adjuvant system were more broadly cross-reactive than antibodies raised against the same epitope conjugated to tetanus toxoid using Adjuvax adjuvant. The method described here is useful for detailed characterization of the interaction of polyclonal antibodies with a panel of synthetic peptide ligands with the objective of obtaining high affinity and cross-reactive antibodies in vaccine development.
Alimentación de Odocoileus virginianus, (Venado de cola blanca) en la localidad El Tibisí, de la Empresa Forestal Integral (EFI)Minas, Pinar del Río, Cuba (2012)

This research about the feeding of the white-tailed deer was carried out at the locality of El Tibisi, Integral Forest Company of Las Minas, and it was aimed at evaluating the possible food sources in four vegetable formations (gallery forest, natural formation of Pinus tropicalis, plantation of Pinus caribaea and natural formation of pine-encino). For the realization of the research, 8 parcels were selected at each vegetable formation. Starting from its center, each parcel was devided into 4 rectangular –11,20 m long by 1,50 m wide–subparcels (128 altogether). In each subparcel, the pruned plants were identified, as well as their pruning frequency and the number of times each plant appeared although not having been pruned, with the purpose of determining the index of alimentary selectivity; to do so, the Index of Jacobs was used. The study also includes an analysis of the stomach content. It was verified that the white-tailed deer uses for feeding a total of 25 species of plants in the four
vegetable formations; being the species Davilla rugosa (Bejuco Colorado de frutos amarillos); Coccocypselum guianensis (Oro Azul); Alibertia edulis (Pitajoni) y Faramea occidentalis (Cafetillo), the ones with the highest index of exploitation and therefore the tastiest. The gallery forest resulted to be the vegetable formation with the highest quantity of alimentary plants consumed by the deer.
XL184 (cabozantinib) for medullary thyroid carcinoma (2011)

Multiple receptor tyrosine kinases (RTKs) are concomitantly activated in the same tumor. The blockade of a single RTK may engage compensatory signaling that maintains cell growth. Targeting multiple kinases might overcome both intrinsic and acquired resistance to antitumoral drugs.
Molecular Identification and Characterization of the Arabidopsis Δ3,5,Δ2,4-Dienoyl-Coenzyme A Isomerase, a Peroxisomal Enzyme Participating in the β-Oxidation Cycle of Unsaturated Fatty Acids (2005)

Degradation of unsaturated fatty acids through the peroxisomal beta-oxidation pathway requires the participation of auxiliary enzymes in addition to the enzymes of the core beta-oxidation cycle. The auxiliary enzyme delta(3,5),delta(2,4)-dienoyl-coenzyme A (CoA) isomerase has been well studied in yeast (Saccharomyces cerevisiae) and mammals, but no plant homolog had been identified and characterized at the biochemical or molecular level. A candidate gene (At5g43280) was identified in Arabidopsis (Arabidopsis thaliana) encoding a protein showing homology to the rat (Rattus norvegicus) delta(3,5),delta(2,4)-dienoyl-CoA isomerase, and possessing an enoyl-CoA hydratase/isomerase fingerprint as well as aspartic and glutamic residues shown to be important for catalytic activity of the mammalian enzyme. The protein, named AtDCI1, contains a peroxisome targeting sequence at the C terminus, and fusion of a fluorescent protein to AtDCI1 directed the chimeric protein to the peroxisome in onion (Allium cepa) cells. AtDCI1 expressed in Escherichia coli was shown to have delta(3,5),delta(2,4)-dienoyl-CoA isomerase activity in vitro. Furthermore, using the synthesis of polyhydroxyalkanoate in yeast peroxisomes as an analytical tool to study the beta-oxidation cycle, expression of AtDCI1 was shown to complement the yeast mutant deficient in the delta(3,5),delta(2,4)-dienoyl-CoA isomerase, thus showing that AtDCI1 is also appropriately targeted to the peroxisome in yeast and has delta(3,5),delta(2,4)-dienoyl-CoA isomerase activity in vivo. The AtDCI1 gene is expressed constitutively in several tissues, but expression is particularly induced during seed germination. Proteins showing high homology with AtDCI1 are found in gymnosperms as well as angiosperms belonging to the Monocotyledon or Dicotyledon classes.
Ras activation of genes: Mob-1 as a model. (1994)

The ras oncogenes function by indirectly controlling expression of a subset of yet-undefined genes that are crucial for cell growth and differentiation. In a differential display strategy, numerous genes were identified on the basis of their differential expression in rat embryo fibroblasts transformed by the cooperation of mutant Ha-ras and p53 genes. We demonstrate here that one such gene, designated mob-1, is a downstream target of the Ras signaling pathway. The 417-bp mob-1 promoter, which contains dual NF-kappa B and AP-1 binding sites, confers the Ras inducibility. Oncogenic Ras as well as serum growth factors that activate endogenous Ras can induce mob-1 expression, but with a fundamental difference in that the oncogenic induction is constitutive whereas the serum induction is transient. mob-1 encodes a small secretory protein with a high degree of homology to IP-10, a member of a proinflammatory cytokine family. These findings link chronic inflammatory response to constitutive ras activation and tumorigenesis. Mob-1 may serve as a secreted marker for oncogenic Ha-ras mutations.
On the Structure of the T-cell Receptor for Antigen (1977)

Antigen-binding receptors of T lymphocytes were analyzed in two different ways. First, the idiotypic properties of T helper cells are studied using anti-idiotypic antisera prepared against isolated antibodies specific for A-CHO. These anti-idiotypic antisera are defined by immunogenetic and immunochemical means with respect to their reactivity with heavy- or light-chain-associated idiotypic determinants. Second, antigen-binding receptors are isolated from enriched T-and B-lymphocyte preparations and compared with respect to their reactivity with antigen and with class- or allotype-specific anti-Ig antisera. The results provide an incomplete picture of the T-cell receptor which shares with antibodies the variable region of the heavy chain but probably no other variable or constant portion.
Ancestral Exonic Organization of FUT8, the Gene Encoding the α6-Fucosyltransferase, Reveals Successive Peptide Domains Which Suggest a Particular Three-Dimensional Core Structure for the α6-Fucosyltransferase Family (2000)

Based on PCR strategies and expression studies, we define the genomic organization of the FUT8b gene. This gene encodes the only known mammalian enzyme transferring fucose in an alpha1-->6 linkage on the asparagine-branched GlcNAc residue of the chitobiose unit of complex N:-glycans. The intron/exon organization of the bovine coding sequence determines five successive functional domains. The first exon encodes a domain homologous to cytoskeleton proteins, the second presents a proline-rich region including a motif XPXPPYXP similar to the peptide ligand of the SH3-domain proteins, the third encodes a gyrase-like domain (an enzyme which can bind nucleotides), and the fourth encodes a peptide sequence homologous to the catalytic domain of proteins transferring sugars. Finally, the last exon encodes a domain homologous to the SH3 conserved motif of the SH2-SH3 protein family. This organization suggests that intramolecular interactions might give a tulip-shaped scaffolding, including the catalytic pocket of the enzyme in the Golgi lumen. Deduced from the published sequence of chromosome 14 (AL109847), the human gene organization of FUT8 seems to be similar to that of bovine FUT8b, although the exon partition is more pronounced (bovine exons 1 and 2 correspond to human exons 1-6). The mosaicism and phylogenetic positions of the alpha6-fucosyltransferase genes are compared with those of other fucosyltransferase genes.
Determinant selection in murine experimental autoimmune myasthenia gravis. Effect of the bm12 mutation on T cell recognition of acetylcholine receptor epitopes (1991)

C57BL/6 (B6) mice respond to immunization with acetylcholine receptor (AChR) from Torpedo californica as measured by T cell proliferation, antibody production, and the development of muscle weakness resembling human myasthenia gravis. The congenic strain B6.C-H-2bm12 (bm12), which differs from B6 by three amino acid substitutions in the beta-chain of the MHC class II molecule I-A, develops a T cell proliferative response but does not produce antibody or develop muscle weakness. By examining the fine specificity of the B6 and bm12 T cell responses to AChR by using T cell clones and synthetic AChR peptides, we found key differences between the two strains in T cell epitope recognition. B6 T cells responded predominantly to the peptide representing alpha-subunit residues 146-162; this response was cross-reactive at the clonal level to peptide 111-126. Based on the sequence homology between these peptides and the T cell response to a set of truncated peptides, the major B6 T cell epitope was determined to be residues 148-152. The cross-reactivity of peptides 146-162 and 111-126 could also be demonstrated in vivo. Immunization of B6 mice with either peptide primed for T cell responses to both peptides. In contrast, immunization of bm12 mice with peptide 111-126 primed for an anti-peptide response, which did not cross-react with 146-162. Peptide-reactive T cells were not elicited after immunization of bm12 mice with 146-162. These results define a major T cell fine specificity in experimental autoimmune myasthenia gravis-susceptible B6 mice to be directed at alpha-subunit residues 148-152. T cells from disease-resistant bm12 mice fail to recognize this epitope but do recognize other portions of AChR. We postulate that alpha-148-152 is a disease-related epitope in murine experimental autoimmune myasthenia gravis. In this informative strain combination, MHC class II-associated determinant selection, rather than Ag responsiveness per se, may play a major role in determining disease susceptibility.
Optical performance monitoring in reconfigurable WDM optical networks using subcarrier multiplexing (2000)

Optical performance monitoring (OPM) is an important approach to determine the quality of optical channels within an optical core network without passing data through optoelectronic regeneration at the monitor points. Using this approach, the quality or "health" of signals can be determined at arbitrary points in a network without knowledge of the transport history of the data or the details of the transmission path. We report experimental results on the use of subcarrier multiplexing (SCM) to perform a variety of monitoring functions including chromatic dispersion monitoring, wavelength registration, power monitoring, and signal-to-noise ratio (SNR) monitoring.
Hyperuniformity, quasi-long-range correlations, and void-space constraints in maximally random jammed particle packings. II. Anisotropy in particle shape (2011)

We extend the results from the first part of this series of two papers by examining hyperuniformity in heterogeneous media composed of impenetrable anisotropic inclusions. Specifically, we consider maximally random jammed (MRJ) packings of hard ellipses and superdisks and show that these systems both possess vanishing infinite-wavelength local-volume-fraction fluctuations and quasi-long-range pair correlations scaling as r(-(d+1)) in d Euclidean dimensions. Our results suggest a strong generalization of a conjecture by Torquato and Stillinger [Phys. Rev. E 68, 041113 (2003)], namely, that all strictly jammed saturated packings of hard particles, including those with size and shape distributions, are hyperuniform with signature quasi-long-range correlations. We show that our arguments concerning the constrained distribution of the void space in MRJ packings directly extend to hard-ellipse and superdisk packings, thereby providing a direct structural explanation for the appearance of hyperuniformity and quasi-long-range correlations in these systems. Additionally, we examine general heterogeneous media with anisotropic inclusions and show unexpectedly that one can decorate a periodic point pattern to obtain a hard-particle system that is not hyperuniform with respect to local-volume-fraction fluctuations. This apparent discrepancy can also be rationalized by appealing to the irregular distribution of the void space arising from the anisotropic shapes of the particles. Our work suggests the intriguing possibility that the MRJ states of hard particles share certain universal features independent of the local properties of the packings, including the packing fraction and average contact number per particle.
Assessment of acute kidney injury in rhabdomyolytic mice by transcutaneous measurement of sinistrin excretion (2016)

Taken together, the results of this study provide important insights into the pathophysiology of kidney injury in rhabdomyolytic mice, and indicate that the transcutaneous measurement of FITC-sinistrin is an efficient and simple method to assess renal function precisely. This method also allows reduction of the required number of experimental animals by monitoring the same mouse over time.
A recombinant bispecific single-chain antibody, CD19 × CD3, induces rapid and high lymphoma-directed cytotoxicity by unstimulated T lymphocytes (2000)

Abstract Although bispecific antibodies directed against malignant lymphoma have been shown to be effective in vitro and in vivo, extended clinical trials so far have been hampered by the fact that conventional approaches to produce these antibodies suffer from low yields, ill-defined byproducts, or laborious purification procedures. To overcome this problem, we have generated a small, recombinant, lymphoma-directed, bispecific single-chain (bsc) antibody according to a novel technique recently described. The antibody consists of 2 different single-chain Fv fragments joined by a glycine-serine linker. One specificity is directed against the CD3 antigen of human T cells, and the other antigen-binding site engages the pan–B-cell marker CD19, uniformly expressed on the vast majority of B-cell malignancies. The construct was expressed in Chinese hamster ovary cells and purified by its C-terminal histioline tag. Specific binding to CD19 and CD3 was demonstrated by fluorescence-activated cell sorter analysis. By redirecting unstimulated primary human T cells derived from the peripheral blood against CD19-positive lymphoma cells, the bscCD19 × CD3 antibody showed significant cytotoxic activity at very low concentrations of 10 to 100 pg/mL and at effector to target cell ratios as low as 2:1. Moreover, strong lymphoma-directed cytotoxicity at low antibody concentrations was rapidly induced during 4 hours even in experiments without any T-cell prestimulation. Thus, this particular antibody proves to be much more efficacious than the bispecific antibodies described until now. Therefore, the described bscCD19 × CD3 molecule should be a suitable candidate to prove the therapeutic benefit of bispecific antibodies in the treatment of non-Hodgkin lymphoma.