gebhart/patrepeval huggingface dataset:
Brillouin-Enhanced Hyperparametric Generation of an Optical Frequency Comb in a Monolithic Highly Nonlinear Fiber Cavity Pumped by a cw Laser (2009)

We demonstrate self-seeded generation of a broadband comb in a highly nonlinear fiber resonator. When pumped with a cw laser, the fiber cavity generates a comb with two characteristic spacings. Hyperparametric modes spaced by approximately 2 THz create the base structure of the comb, while commensurate Brillouin modes spaced by approximately 10 GHz populate the intermediate frequency gaps. The frequency modes are coherent, and the repetition rate of the comb has been locked to a microwave standard.
Metallkomplexe mit biologisch wichtigen Liganden, CIV [1]. ortho-Palladierte Komplexe von N,N-Dimethyl-C-phenyl-glycinmethylester. Synthese von α-Aminosäure-Derivaten durch Insertion von Isocyaniden, CO, Alkenen und Alkinen in die Pd-C-Bindung / Metal Complexes of Biologically Important Ligands, CIV [ 1]. ortho-Palladated Complexes of N,N-Dimethyl-C-phenylglycine-methylester. Synthesis of α-Amino Acid Derivatives by Insertion of Isocyanides, CO, Alkenes, and Alkynes into the Pd-C Bond (1998)

Abstract N,N-Dimethyl-C-phenylglycinemethylester reacts with Pd(OAc) 2 in acetic acid to give the orthopalladated, acetato bridged complex 1. Treatment of 1 with sodium halide affords the chloro, bromo, and iodo bridged compounds [Me 2 NC(H)(CO 2 Me)C 6 H 4 PdX] 2 (2a -c) (X = halide). From 2a and 1,1′-bis(diphenylphosphino)ferrocene the phosphine bridged trinuclear complex 3 is obtained. Substitution of the amine ligand of 2a by the phosphino group is observed for the reaction of 2a with Ph 2 PC(Me)C(Me)PPh 2 . Insertion of 2,6-dimethyl-phenylisocyanide, CO, alkyl-vinyl-ketones, and diphenylacetylene into the Pd-C bond o f 2a -c provides the orthosubstituted organic and organometallic derivatives of phenylglycine 6a -c, 7, 8a -b and 9a -c. The crystal structures of 1, 4a, 6a, 7 and 9a were determined by X-ray diffraction.
Factors Affecting Agrobacterium-mediated Transformation of Plants (2008)

Plant transformation technology has become a versatile platform for cultivar improvement as well as for studying gene function in plants. The development of an efficient method for genetic transformation is a prerequisite for the application of molecular biology to the improvement of a given crop species. Agrobacterium-mediated genetic transformation is the dominant technology used for the production of genetically modified transgenic plants. Extensive research aimed at improving the molecular machinery of Agrobacterium responsible for the generation and transport of the bacterial DNA into the host cell has resulted in the establishment of many recombinant Agrobacterium strains and technologies currently used for the successful transformation of numerous plant species. Many factors influencing Agrobacterium-mediated transformation of plants have been investigated and elucidated. These factors include bacterial strains and cell density, plant species and genotype, plant growth regulators and antibiotics, explant, explant wounding, light and temperature. Before attempting stable transformation of any new species, it is useful to optimize the factors influencing transformation efficiency, as this can reduce future costs in labor and materials. The studies of such factors hold great promise for the future of plant biotechnology and plant genetic engineering as they might help in the development of conceptually new techniques and approaches needed today to expand the host range of Agrobacterium and to control the transformation process and its outcome during the production of transgenic plants. Here, I review some of the main factors that influence Agrobacterium-mediated genetic transformation and discuss their possible roles in this process.
On the Meaning of Affinity:  Cluster Glycoside Effects and Concanavalin A (1999)

The inhibition of protein−carbohydrate interaction provides a powerful therapeutic strategy for the treatment of myriad human diseases. To date, application of such approaches have been frustrated by the inherent low affinity of carbohydrate ligands for their protein receptors. Because lectins typically exist in multimeric assemblies, a variety of polyvalent saccharide ligands have been prepared in the search for high affinity. The cluster glycoside effect, or the observation of high affinity derived from multivalency in oligosaccharide ligands, apparently represents the best strategy for overcoming the “weak binding” problem. Here we report the synthesis of a series of multivalent dendritic saccharides and a biophysical evaluation of their interaction with the plant lectin concanavalin A. Although a 30-fold enhancement in affinity on a valence-corrected basis is observed by agglutination assay, calorimetric titration of soluble protein with a range of multivalent ligands reveals no enhancement in binding free energies. Rather, IC50 values from agglutination measurements correlate well with entropies of binding. This observation suggests that hemagglutination measures a phenomenon distinct from binding that is typified by a large favorable entropy and an unfavorable enthalpy: this process is almost certainly aggregation. Supporting this assertion, we report crystal structures of multivalent ligands cross-linking concanavalin A dimers. To the best of our knowledge, these structures are the first reported of their kind. Our results indicate that hemagglutination assays evaluate the ability of ligands to inhibit the formation of cross-linked lattices, a process only tangentially related to reversible ligand binding. Cluster glycoside effects observed in agglutination assays must, therefore, be viewed with caution. Such effects may or may not be relevant to the design of therapeutically useful saccharides.
Preparation of TADOOH, a Hydroperoxide from TADDOL, and Use in Highly Enantioface- and Enantiomer-Differentiating Oxidations (2001)

Replacement of one OH group in TADDOL (=α,α,α′,α′-tetraaryl-1,3-dioxolane-4,5-dimethanol) by an OOH group gives a stable, crystalline chiral hydroperoxy alcohol TADOOH (={(4R,5R)-5-[(hydroperoxydiphenyl)methyl]-2,2-dimethyl-1,3-dioxolan-4-yl}diphenylmethanol) 3, the crystal structure of which resembles those of numerous other TADDOL derivatives (Fig. 2). The new hydroperoxide was tested as chiral oxidant in three types of reactions: the epoxidation of enones with base catalysis (Scheme 2), the sulfoxidation of methyl phenyl sulfide (Scheme 3), and the Baeyer-Villiger oxidation of bicyclic and tricyclic cyclobutanones, rac-10a – d with kinetic resolution (Scheme 4, Fig. 3, and Table). Products of up to 99% enantiomer puritiy were isolated (the highest values yet observed for oxidations with a chiral hydroperoxide!). Mechanistic models are proposed for the stereochemical courses of the three types of reactions (Schemes 5 and 6, and Fig. 4). Results of AM1 calculations of the relative transition-state energies for the anionic rearrangements of the exo Criegee adducts of TADOOH to the enantiomeric bicyclo[3.2.0]heptan-6-ones are in qualitative agreement with the observed relative rates (Table and Fig. 5).
Compactly supported functions (2004)

In numerical analysis, the concept of locally supported basis functions is of general importance. Several function spaces used for approximation possess locally supported basis functions. The most prominent examples in the one-dimensional case are the well-known B-splines. The general advantages of compactly supported basis functions are a sparse interpolation matrix on the one hand, and the possibility of a fast evaluation of the interpolant on the other.
Preparation of 1-Aryl-5-(<i>N</i>-aryl-<i>N</i>-benzoylamino)tetrazoles (1987)

The synthesis of 1-aryl-5-(N-aryl-N-benzoylamino) tetrazoles from diarylcarbodiimides, azide ion, and benzoyl chloride using solid-liquid phase-transfer catalysis is reported.
An ultra low-power RF bipolar technology on glass (2002)

We present a new technology, SOA (Silicon-On-Anything) to transfer circuits processed on SOI substrates to another substrate, e.g. glass or alumina. We have used this technology to integrate an ultra low-power bipolar high-frequency process with high-quality passive components including spiral inductors. Circuits with record low-power RF performance are demonstrated.
Hematologic engraftment and immune reconstitution posttransplantation with anti-B1 purged autologous bone marrow (1987)

Hematologic engraftment and immune reconstitution were examined in patients who received cyclophosphamide and total body irradiation therapy followed by infusion of autologous bone marrow purged with anti-B1 monoclonal antibody (MoAb) and complement as therapy for non-Hodgkin's lymphoma. Hematologic engraftment was prompt with return of greater than or equal to 0.5 X 10(3)/microL granulocytes and greater than or equal to 2 X 10(4)/microL platelets at a median of 26 and 29 days posttransplant, respectively. Immunologic reconstitution, in contrast, was prolonged. Normal numbers of circulating B cells were consistently noted by five months posttransplant, whereas return of normal immunoglobulin levels in some patients did not occur for one year. Normal numbers of T cells were evident within the first month posttransplant, but a reversed T4:T8 ratio persisted in some patients up to three years. In vitro responses of either B cells to triggers of activation or of T cells to mitogens and antigens were not normal for at least three months posttransplant. Natural killer (NK) cells predominated early after transplant and may demonstrate cytotoxicity against tumor cells. Our studies demonstrate that transplantation with anti-B1 purged autologous bone marrow results in complete hematologic and delayed immunologic engraftment. No significant acute or chronic clinical toxicities have been observed.
Murine and human pluripotent stem cell-derived cardiac bodies form contractile myocardial tissue in vitro (2012)

BCT with contractile forces comparable with native myocardium can be generated from enriched, PSC-derived CMs, based on a novel concept of tissue formation from non-dissociated cardiac cell aggregates. In combination with the successful generation of tissue using a defined animal-free matrix, this represents a major step towards clinical applicability of stem cell-based heart tissue for myocardial repair.
A Novel Macrophage Actin-associated Protein (MAYP) Is Tyrosine-phosphorylated following Colony Stimulating Factor-1 Stimulation (1998)

An approximately 37-kDa cytoplasmic protein is rapidly tyrosine-phosphorylated in the response of mouse BAC1.2F5 macrophages to colony stimulating factor-1 (CSF-1). pp37 was purified from the cytosolic fraction by anti-Tyr(P) affinity chromatography, size exclusion chromatography, and C4 reverse phase high pressure liquid chromatography. The sequences of four peptides derived from the purified protein matched portions of an expressed sequence tag (EST) sequence, and the EST clone was used to obtain cDNA clones encoding the pp37 protein, which shares sequence similarity with the PST PIP (proline, serine, threonine phosphatase interacting protein)/CDC15 family of protein-tyrosine phosphatase substrates. pp37 is predicted to contain a Fes/CIP4 homology (FCH) domain and an actin-binding domain-like sequence. It is expressed selectively in macrophages, macrophage cell lines, and at low levels in macrophage-containing tissues. pp37 is predominantly found in the cytosol, where it is associated with actin. However, approximately 4% resides in the membrane fraction, and the trace amount in the cytoskeletal fraction is increased by CSF-1 stimulation. Termed macrophage actin-associated tyrosine-phosphorylated protein (MAYP), p37 is the major F-actin-associated protein that is tyrosine-phosphorylated in macrophages and is likely to play a role in regulating the CSF-1-induced reorganization of the actin cytoskeleton.
Cavitation : A technology on the horizon (2006)

An overview of the application of cavitation phenomenon for the intensification of chemical/physical processing applications has been presented here, discussing the causes for the observed enhancement and highlighting some of the typical examples. The important considerations required for efficient scale-up of the cavitational reactors and subsequent industrial applications have been depicted based on the work carried out as a result of sponsored projects at the Institute of Chemical Technology, Mumbai. Overall, it appears that the combined efforts of physicists, chemists and chemical engineers are required to effectively use cavitational reactors for industrial applications. Some recommendations for further work to be carried out in this area have also been mentioned, which should allow the exploitation of this technology on an industrial scale.
Dynamic multipath mitigation applying unscented Kalman filters in local positioning systems (2011)

Multipath propagation is still one of the major problems in local positioning systems today. Especially in indoor environments, the received signals are disturbed by blockages and reflections. This can lead to a large bias in the user's time-of-arrival (TOA) value. Thus multipath is the most dominant error source for positioning. In order to improve the positioning performance in multipath environments, recent multipath mitigation algorithms based upon the concept of sequential Bayesian estimation are used. The presented approach tries to overcome the multipath problem by estimating the channel dynamics, using unscented Kalman filters (UKF). Simulations on artificial and measured channels from indoor as well as outdoor environments show the profit of the proposed estimator model. Furthermore, the quality of channel estimation applying the UKF and the channel sounding capabilities of the estimator are shown.
DNA end joining becomes less efficient and more error-prone during cellular senescence (2004)

Accumulation of somatic mutations is thought to contribute to the aging process. Genomic instability has been shown to increase during aging, suggesting an aberrant function of DNA double-strand break (DSB) repair. Surprisingly, DSB repair has not been examined with respect to cellular senescence. Therefore, we have studied the ability of young, presenescent, and senescent normal human fibroblasts to repair DSBs in transfected DNA by using a fluorescent reporter substrate. We have found that the efficiency of end joining is reduced up to 4.5 fold in presenescent and senescent cells, relative to young cells. Sequence analysis of end junctions showed that the frequency of precise ligation was higher in young cells, whereas end joining in old cells was associated with extended deletions. These results indicate that end joining becomes inefficient and more error-prone during cellular senescence. Furthermore, the ability to use microhomologies for end joining was compromised in senescent cells, suggesting that young and senescent cells may use different end joining pathways. We hypothesize that inefficient and aberrant end joining is a likely mechanism underlying the age-related genomic instability and higher incidence of cancer in the elderly.
Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production (2008)

Producing complex chemicals using synthetic metabolic pathways in microbial hosts can have many advantages over chemical synthesis but is often complicated by deleterious interactions between pathway intermediates and the host cell metabolism. With the maturation of functional genomic analysis, it is now technically feasible to identify modes of toxicity associated with the accumulation of foreign molecules in the engineered bacterium. Previously, Escherichia coli was engineered to produce large quantities of isoprenoids by creating a mevalonate-based isopentenyl pyrophosphate biosynthetic pathway (V. J. J. Martin et al., Nat. Biotechnol. 21:796-802, 2003). The engineered E. coli strain produced high levels of isoprenoids, but further optimization led to an imbalance in carbon flux and the accumulation of the pathway intermediate 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA), which proved to be cytotoxic to E. coli. Using both DNA microarray analysis and targeted metabolite profiling, we have studied E. coli strains inhibited by the intracellular accumulation of HMG-CoA. Our results indicate that HMG-CoA inhibits fatty acid biosynthesis in the microbial host, leading to generalized membrane stress. The cytotoxic effects of HMG-CoA accumulation can be counteracted by the addition of palmitic acid (16:0) and, to a lesser extent, oleic acid (cis-Delta(9)-18:1) in the growth medium. This work demonstrates the utility of using transcriptomic and metabolomic methods to optimize synthetic biological systems.
Growth of Ultrahigh Density Vertically Aligned Carbon Nanotube Forests for Interconnects (2010)

We present a general catalyst design to synthesize ultrahigh density, aligned forests of carbon nanotubes by cyclic deposition and annealing of catalyst thin films. This leads to nanotube forests with an area density of at least 10(13) cm(-2), over 1 order of magnitude higher than existing values, and close to the limit of a fully dense forest. The technique consists of cycles of ultrathin metal film deposition, annealing, and immobilization. These ultradense forests are needed to use carbon nanotubes as vias and interconnects in integrated circuits and thermal interface materials. Further density increase to 10(14) cm(-2) by reducing nanotube diameter is possible, and it is also applicable to nanowires.
Introduction (1991)

This chapter explains and examines the changes in the theory and practice of critical writing. It describes the nature of institutional and intellectual authority in critical discourse in the final decades of the nineteenth century. It examines the sociology of knowledge in Britain from the 1870s to the 1890s. It argues that such a methodology might possess a general applicability, particularly for understanding the practice of literary criticism at the present time.
Structure of the Shiga-like Toxin I B-Pentamer Complexed with an Analogue of Its Receptor Gb<sub>3</sub><sup>,</sup> (1998)

Shiga-like toxin I (SLT-I) is a virulence factor of Escherichia coli strains that cause disease in humans. Like other members of the Shiga toxin family, it consists of an enzymatic (A) subunit and five copies of a binding subunit (the B-pentamer). The B-pentamer binds to a specific glycolipid, globotriaosylceramide (Gb3), on the surface of target cells and thereby plays a crucial role in the entry of the toxin. Here we present the crystal structure at 2.8 A resolution of the SLT-I B-pentamer complexed with an analogue of the Gb3 trisaccharide. The structure reveals a surprising density of binding sites, with three trisaccharide molecules bound to each B-subunit monomer of 69 residues. All 15 trisaccharides bind to one side of the B-pentamer, providing further evidence that this side faces the cell membrane. The structural model is consistent with data from site-directed mutagenesis and binding of carbohydrate analogues, and allows the rational design of therapeutic Gb3 analogues that block the attachment of toxin to cells.
Subcellular distribution of the R‐subunits of cAMP‐dependent protein kinase in LS‐174T human colon carcinoma cells (1998)

Abstract The analysis of the particulate preparations of LS‐174T human colon carcinoma cells in confluent stage of growth revealed different distribution for regulatory subunits (R) of cAMP‐dependent protein kinase (PKA) in the subcellular compartments. The LS‐174T cell lysates were subjected to differential and discontinuous sucrose density gradient centrifugation. The obtained fractions were assayed for marker enzymes and photoaffinity labeled with 8‐N3[32P]cAMP. The whole lysates and cytoplasmic fraction exhibited the presence of both RIα and RIIα ‐ subunits of PKA. The fractions exhibiting high activity of the marker enzymes for plasma membranes, Golgi apparatus and mitochondria contained mainly RIIα. In the fractions of lysosomes and microsomes RIα and RIIα were found in nearly equal amounts.
Directed evolution: Past, present, and future (2012)

Directed evolution, the laboratory process by which biological entities with desired traits are created through iterative rounds of genetic diversification and library screening or selection, has become one of the most useful and widespread tools in basic and applied biology. From its roots in classical strain engineering and adaptive evolution, modern directed evolution came of age twenty years ago with the demonstration of repeated rounds of PCR-driven random mutagenesis and activity screening to improve protein properties. Since then, numerous techniques have been developed that have enabled the evolution of virtually any protein, pathway, network or entire organism of interest. Here we recount some of the major milestones in the history of directed evolution, highlight the most promising recent developments in the field, and discuss the future challenges and opportunities that lie ahead.
High‐yield secretion of recombinant gelatins by Pichia pastoris (1999)

Recombinant non-hydroxylated gelatins based on mouse type I and rat type III collagen sequences were secreted from the methylotrophic yeast Pichia pastoris, using the Saccharomyces cerevisiae α-mating factor prepro signal. Proteolytic degradation could be minimized to a large extent by performing fermentations at pH 3·0 and by adding casamino acids to the medium, even though gelatin is extremely susceptible to proteolysis due to its open, unfolded structure. Proteolytic cleavage at specific mono-arginylic sites, by a putative Kex2-like protease, could be successfully abolished by site-directed mutagenesis of these sites. Production levels as high as 14·8 g/l clarified both were obtained, using multicopy tranformants. To our knowledge, this represents the highest level of heterologous protein secretion reported to date for P. pastoris. Copyright © 1999 John Wiley & Sons, Ltd.
Cloning and expression of the Pasteurella multocida toxin gene, toxA, in Escherichia coli (1989)

A chromosomal DNA library of a toxigenic type D strain of Pasteurella multocida subsp. multocida was established in Escherichia coli. From this library two clones, SPE308 and SPE312, were identified by using a monoclonal antibody against the osteoclast-stimulating P. multocida toxin (PMT). Extracts of these clones showed cytopathic activity identical to that of extracts of toxigenic P. multocida. The recombinant plasmids, pSPE308 and pSPE312, directed the synthesis of a protein with an apparent molecular weight of 143,000 which could be specifically detected by anti-PMT antibody. The recombinant toxin, which was located in the cytoplasm of E. coli, was purified by affinity chromatography with immobilized monoclonal antibody and was shown to react in a manner identical to that of PMT in a quantitative structural test using a series of monoclonal antibodies as well as in all quantitative functional tests used, i.e., tests for dermonecrotic activity and mouse lethality and the embryonic bovine lung cell test for cytopathic activity. The gene encoding this toxic activity was named toxA and was found to be present in the chromosome of toxigenic strains only of P. multocida. A probe spanning the toxA gene therefore has potential in the diagnosis and surveillance of progressive atrophic rhinitis in pigs.