gebhart/patrepeval huggingface dataset:
Engineering Thermoacidophilic Archaea using Linear DNA Recombination (2011)

Thermoacidophilic archaea comprise one of the major classes of extremophiles. Most belong to the family Sulfolobales within the phylum Crenarchaeota. They are of applied interest as sources of hyperstable enzymes, for biomining of base and precious metals, and for evolutionary studies because of their use of eukaryotic-like subcellular mechanisms. Genetic methods are available for several species particularly Sulfolobus solfataricus. This organism has a considerable number of methods available for the construction of novel cell lines with unique functions. This chapter presents recent developments in the use of homologous recombination and linear DNA for the engineering of site-specific changes in the genome of S. solfataricus.
Sites of specific B cell activation in primary and secondary responses to T cell‐dependent and T cell‐independent antigens (1991)

Techniques which identify hapten-specific B cells in tissues have been used to determine the sites of B cell activation in rat spleens in response to T cell-dependent (TD) antigens and T cell-independent type-1 (TI-1) antigens. Surface-associated hapten binding by specific memory B cells and B blasts was distinguished from the strong cytoplasmic hapten binding by specific plasma cells and plasmablasts. Blast cells in S phase were identified in tissue sections by staining cells which had been pulse labeled in vivo with 5-bromo-2'-deoxyuridine. Hapten-specific B blast cells are found in three sites: (a) around interdigitating cells in the T cell-rich zones; (b) in the follicular dendritic cell network and (c) in association with macrophages in the red pulp. Hapten-binding memory B cells, which are not in cell cycle, accumulate in the marginal zones and to a lesser extent the follicular mantles in response to TD and TI-1 antigens. The hapten-specific blast response in T zones is confined to the first few days after antigen is given and is low for primary responses to TD antigens, but massive on secondary challenge, when marginal zone memory B cells migrate to the T zones. Both the primary and secondary T zone responses to TI-1 antigens are impressive and in these responses hapten-specific B blasts are also found in the splenic red pulp. The follicular response to TD antigens starts with a small number of B blasts (fewer than five) entering each follicle. These increase in number exponentially so that by the 4th day after immunization they fill the follicle. The oligoclonality of the response is shown in simultaneous responses to two haptens where 6%-31% of the follicles on day 3 after immunization contain blasts specific for only one of the two haptens. During the 4th day classical zonal pattern of germinal centers develops. The surface immunoglobulin-positive B blasts are lost from the follicle center, while one pole of the follicular dendritic cell network fills with surface immunoglobulin-negative centroblasts. Centroblasts do not increase in numbers but divide to give rise to centrocytes, which re-express sIg and migrate into the follicular dendritic cell network. Cell kinetic studies indicate that the centrocyte population is renewed from centroblasts every 7 h. Centrocytes either leave the germinal center within this time or die in situ.(ABSTRACT TRUNCATED AT 400 WORDS)
Stroke volume variability and heart rate power spectrum in relation to posture changes in healthy subjects. (2004)

The combined analysis of HRV and SVV revealed different cardiovascular responses to postural stress in the three age groups considered.
Alternative splicing generates functionally distinct N-methyl-D-aspartate receptors. (1992)

We have used expression cloning in Xenopus oocytes to isolate two different cDNAs encoding functional N-methyl-D-aspartate (NMDA) receptor subunits. The two receptors (NMDA-R1A and -R1B) display different pharmacologic properties as a consequence of alternative exon addition within the putative ligand-binding domain. The splicing choice is regulated such that R1B is the predominant form of receptor in the cerebellum, whereas R1A predominates in other brain regions. Expression of either of the subunits alone in oocytes results in an NMDA-evoked inward current with electrophysiologic properties closely resembling those of the NMDA receptors observed in neurons. Thus, the complex properties exhibited by the NMDA receptor in neurons can be generated by the expression of a single receptor subunit.
User Modeling for the Result Re-Ranking in the Meta-Search Engines via Reinforcement Learning (2007)

Today there are thousands of search engines available, so it is difficult for users to know where they are, how to use them and what topics they best address. Meta-search engines reduce the users' burden by dispatching queries to multiple search engines in parallel and combining the returned results. But there are some problems yet. One of them is that, none of them includes the user model in the answer. In this paper, we propose a mechanism to create a mapping between different categories of users and the underlying search engines using the reinforcement learning approach. By this way, the meta-search engine learns to identify which search engines are most appropriate for particular queries from different user models.
Molecular Regulation of Urothelial Renewal and Host Defenses during Infection with Uropathogenic Escherichia coli (2002)

Uropathogenic Escherichia coli (UPEC), the principal cause of urinary tract infection in women, attaches to the superficial facet cell layer of the bladder epithelium (urothelium) via its FimH adhesin. Attachment triggers exfoliation of bacteria-laden superficial facet cells, followed by rapid reconstitution of the urothelium through differentiation of underlying basal and intermediate cells. We have used DNA microarrays to define the molecular regulators of urothelial renewal and host defense expressed in adult C57Bl/6 female mice during the early phases of infection with isogenic virulent (FimH+) or avirulent (FimH-) UPEC strains. The temporal evolution and cellular origins of selected responses were then characterized by real time quantitative reverse transcriptase-PCR, in situ hybridization, and immunohistochemical analyses. Well before exfoliation is evident, FimH-mediated attachment suppresses transforming growth factor-beta (Bmp4) and Wnt5a/Ca(2+) signaling to promote subsequent differentiation of basal/intermediate cells. The early transcriptional responses to attachment also include induction of regulators of proliferation (e.g. epidermal growth factor family members), induction of the ETS transcription factor Elf3, which transactivates genes involved in epithelial differentiation and host defense (inducible nitric-oxide synthase), induction of modulators, and mediators of pro-inflammatory responses (e.g. Socs3, Cebp/delta, Bcl3, and CC/CXC chemokines), induction of modulators of apoptotic responses (A20), and induction of intermediate cell tight junction components (claudin-4). Both early and late phases of the host response exhibit remarkable specificity for the FimH+ strain and provide new insights about the molecular cascade mobilized to combat UPEC-associated urinary tract infection.
Specific globin mRNAs in human erythroleukemia (K562) cells (1984)

Specific globin mRNA accumulation was quantitated in several lines of K562 cells in the absence and the presence of hemin. Using specific cloned DNA probes, the amounts of zeta, alpha, epsilon and gamma mRNAs were shown to be increased 2–3-fold in the presence of 20 microM hemin. No delta- or beta-globin mRNAs were detectable in any of the lines. In one line, Bos, there was a marked decrease in epsilon-globin mRNA, which increased with hemin, although still to much lower levels than in the other lines. The decreased epsilon-globin mRNA accumulation in Bos is shown to be due to decreased epsilon-globin gene transcription.
Early and Delayed Consequences of β <sub>2</sub> -Adrenergic Receptor Overexpression in Mouse Hearts (2000)

These data demonstrate that the heart tolerates enhanced contractile function via 60-fold beta(2)AR overexpression without detriment for a period of >/=1 year and that higher levels of expression result in either aggressive or delayed cardiomyopathy. The consequences for enhanced betaAR function in the heart appear to be highly dependent on which signaling elements are increased and to what extent.
Developing brain and behaviour: the role of lipids in infant formula. (1997)

Clinical Studies: A. Lucas, Long Chain Polyunsaturated Fatty Acids, Infant Feeding and Cognitive Development. S.E. Carlson, Long Chain Polyunsaturated Fatty Acid Supplementation of Preterm Infants. S.M. Innis, Polyunsaturated Fatty Acid Nutrition in Infants Born at Term. W.C. Heird, Statistically Significant Vs. Biologically Significant Effects of Long-Chain Polyunsaturated Fatty Acids on Growth. Methodology: Clinical Studies: L.T. Singer, Methodological Considerations in Longitudinal Studies of Infant Risk. D.L. Mayer and V. Dobson, Grating Acuity Cards: Validity and Reliability in Studies of Human Visual Development. Behavioural Science Considerations: R.B. Mccall and C.W. Mash, Long Chain Polyunsaturated Fatty Acids and the Measurement and Prediction of Intelligence. J. Colombo, Individual Differences in Infant Cognition: Methods, Measures, And Models. P.E. Wainwright and G.R. Ward, Early Nutrition and Behaviour: A Conceptual Framework for Critical Analysis of Research. C.A. Shaw and J.C. Mceachern, The Effects of Early Diet on Synaptic Function and Behaviour: Pitfalls and Potentials. General Commentary on Behavioural Science Implications and Methodology: Appendices: M.H. Bornstein, Nutrition and Development: Observations and Implications. M. Appelbaum, Design, Measurement, And Statistical Approaches. M. Neuringer and S. Reisbick, General Commentary. Subject Index.
The Safe Use of Sodium Hydride on Scale: The Process Development of a Chloropyrimidine Displacement (2011)

Sodium hydride was found to be the best base for a displacement reaction on a chloropyrimidine. Due to the insolubility of sodium hydride in all solvents and high reactivity with atmospheric moisture, solutions dealing with the associated safety concerns on kilogram scale are described. The use of sodium hydride in premeasured dissolvable bag packaging (SecuBags), online process analytical technology (PAT) to monitor the hydrogen off-gas, and the development of analytical methods to monitor residual polymer and potential degradation products allowed for a successful scale-up and on-time delivery of a quality product.
Linear Bi-SQUID Arrays for Electrically Small Antennas (2010)

Recently we proposed so-called bi-SQUID based on a 3-junction SQUID circuit capable of providing highly linear voltage response. In this report, we present the experimental evaluation of series arrays of 20 and 128 bi-SQUIDs fabricated with a 4.5 kA/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> Nb process as well as a prototype of an active electrically small antenna based on series array of 12 bi-SQUIDs. Both the origins of imperfections of the observed response linearity and the possible ways of the linearity improvement are discussed.
The chamber memory effect induces P+ junction leakage and EEPROM tunneling oxide degradation (2003)

In middle of 1998, the failure modes of P+ junction leakage and tunneling oxide degradation on logic products (single poly, single metal 9 V LCD driver products) and EEPROM products (single poly, single metal 5 V EEPROM products) were found. From failure analysis, we found that a chamber memory effect was the root cause. In foundry fabs, an oxide etcher sometimes must run different recipes to meet manufacturing requirements, e.g. contact, spacer and via etching recipes. Due to these mixed recipes running in the same oxide etch chamber, interactive effects of different recipes occur. In this case, a special BiCMOS via etch recipe (recipe A) affected the spacer etch recipe of logic and EEPROM processes. We found that if logic and EEPROM products ran the spacer etch behind the via recipe A in the same chamber, then higher P+ junction leakage can happen on logic and EEPROM products and tunneling oxide degradation can happen on EEPROM products. Our failure analysis showed that CF/sub 4/ gas played a major role in inducing chamber memory effects in via recipe A. Due to process requirements, via recipe A uses CF/sub 4/ only to etch IMD layers to enlarge via size for RC via value reduction. The via etch recipe A with only CF/sub 4/ gas could change the chamber conditions, similar to the chamber dry cleaning recipe in equipment PM. Free F radicals remained in chamber after recipe A was run. When subsequent logic and EEPROM product lots ran spacer etching, contaminant atoms were released from the chamber wall and re-deposited on Si surfaces at source/drain and EEPROM floating gate edge areas. This paper details the failure analysis process.
Evaluation of bleeding disorders (1998)

A single, optimal screening laboratory test for hemostasis would evaluate vascular, platelet, coagulation, and fibrinolytic functions. Unfortunately, such a test does not exist. The key factor in determining the presence of a bleeding diathesis is obtaining a detailed patient history. Results of coagulation tests should always be interpreted in the context of such a history. Screening tests include platelet count, PTT, and PT. Subsequent investigations depend on the results of these tests.
Evaporation-Induced Self-Assembly: NanostructuresEasy (2004)

The following article is an edited transcript based on the MRS Medalist presentation given by C. Jeffrey Brinker (Sandia National Laboratories and the University of New Mexico) on December 3, 2003, at the Materials Research Society Fall Meeting in Boston. Brinker received the Medal for “his pioneering application of principles of sol-gel chemistry to the self-assembly of functional nanoscale materials.” Nature combines hard and soft materials, often in hierarchical architectures, to obtain synergistic, optimized properties with proven, complex functionalities. Emulating natural designs in robust engineering materials using efficient processing approaches represents a fundamental challenge to materials chemists. This presentation reviews progress on understanding so-called evaporation-induced silica/surfactant self-assembly (EISA) as a simple, general means of preparing porous thin-film nanostructures. Such porous materials are of interest for membranes, low-dielectric-constant (low-k) insulators, and even ‘”nano-valves” that open and close in response to an external stimulus. EISA can also be used to simultaneously organize hydrophilic and hydrophobic precursors into hybrid nanocomposites that are optically or chemically polymerizable, patternable, or adjustable.
Environmental Effects on the Femtosecond−Picosecond Fluorescence Dynamics of Photoactive Yellow Protein:  Chromophores in Aqueous Solutions and in Protein Nanospaces Modified by Site-Directed Mutagenesis (1998)

The effect of the protein environment surrounding chromophores (protein nanospaces) on the photoinduced ultrafast twisting of chromophores in photoactive yellow protein (PYP) was investigated by comparing the femtosecond−picosecond fluorescence dynamics of wild type PYP with those of the chromophore in aqueous solution as well as in protein nanospace modified by site-directed mutagenesis. The rate of the twisted state formation of the chromophore (the primary step of the trans → cis photoisomerization) was demonstrated to be considerably enhanced in protein compared with the aqueous solution. Moreover, results of the measurements of fluorescence dynamics of the chromophore in the protein nanospace modified by site-directed mutagenesis implied that the twisted state formation by flipping the thioester linkage of the chromophore was slowed by modifying the nanospace structure to a slightly looser one. Namely, the more restricted structure of the protein nanospace in the wild-type PYP seems to be best engineered for the twisting by the flipping mechanism.
Biosynthesis of 3-Hydroxy-5-Methyl-O-Methyltyrosine in the Saframycin/Safracin Biosynthetic Pathway (2008)

The biosynthesis study of antibiotics saframycin (SFM) in Streptomyces lavendulae and safracin (SAC) in Pseudomonas fluorescens demonstrated that 3-hydroxy-5-methyl-Omethyltyrosine (3h5mOmTyr), a nonproteinogenic amino acid, is the precursor of the tetrahydroisoquinoline molecular core. In the biosynthetic gene cluster of SAC/SFM, sacD/ sfmD encodes a protein with high homology to each other but no sequence similarity to other known enzymes; sacF/ sfmM2 and sacG/sfmM3 encode methyltransferases for Cmethylation and O-methylation; and sacE/sfmF encodes a small protein with significant sequence similarity to the MbtH-like proteins, which are frequently found in the biosynthetic pathways of nonribosomal peptide antibiotics and siderophores. To address their function, the biosynthetic cassette of 3h5mOmTyr was heterologously expressed in S. coelicolor and P. putida, and an in-frame deletion and complementation in trans were carried out. The results revealed that (i) SfmD catalyzes the hydroxylation of aromatic rings;(ii) sacD/sacF/sacG in the SAC gene cluster and sfmD/sfmM2/sfmM3 in the SFM cluster are sufficient for the biosynthesis of 3h5mOmTyr; and (iii) the mbtH-like gene is not required for the biosynthesis of the 3h5mOmTyr precursor.
Relationship between Surface Scattering and Microtopographic Features (1979)

In the smooth-surface limit, the angular distribution of the light scattered from a surface maps the power spectral density of its residual surface roughness. This result is essentially independent of the scattering theory used and the statistical properties of the surface roughness. The power spectral densities of engineering surfaces are generally broad and increase with increasing spatial wavelength. As a result, practical surface finish parameters are not intrinsic properties of the surface, but depend, with varying degrees of sensitivity, on the bandwidth limits inherent in their measurement or dictated by their application. These issues are discussed with reference to two classes of finish parameters: those related to the central moments of the scattering spectrum, and those related to the coefficients in the expansion of the shape of the spectrum in inverse powers of the scattering angle. The significance of "1/02" scattering in this context is emphasized. A shot model of surface roughness is then introduced to gain further insight into the relationship between scattering and surface features. In this model inverse power terms are related to "edge" scattering effects from critical points in various types of elemental microdefects. The relationship between this view and electronic noise is pointed out; in particular, the correspondence between "1/02" scattering and "1/f" or flicker-noise phenomena.
Gymnasterkoreaynes A−F, Cytotoxic Polyacetylenes from <i>Gymnaster </i><i>k</i><i>oraiensis</i> (2002)

Six new polyacetylenes, gymnasterkoreaynes A-F (1-6), were isolated from the roots of Gymnaster koraiensis, together with 2,9,16-heptadecatrien-4,6-diyn-8-ol (7) and 1,9,16-heptadecatriene-4,6-diyn-3,8-diol (8), by bioassay-guided fractionation using the L1210 tumor cell line as a model for cytotoxicity. The structures of compounds 1-6 were established spectroscopically, which included 2D NMR experiments. Gymnasterkoreaynes A-F (1-6) are linear diacetylenes and are structurally related to falcarinol, panaxynol, panaxydiol, and panaxytriol. Of the compounds isolated, gymnasterkoreaynes B (2), C (3), F (6), and 1,9,16-heptadecatrien-4,6-diyn-3,8-diol (8) exhibited significant cytotoxicity against L1210 tumor cells with ED(50) values of 0.12-3.3 microg/mL.
On identifying representative relevant documents (2010)

Using relevance feedback can significantly improve the effectiveness of ad hoc (query-based) retrieval. However, retrieval performance can significantly vary with respect to the given set of relevant documents. Our goal is to establish a quantitative analysis of what makes a relevant document a good representative of the relevant-documents set regardless of the retrieval approach employed. That is, we would like to estimate the extent to which a relevant document can effectively help in finding (other) relevant documents using some relevance-feedback method employed over the corpus. We present various representativeness estimates; some of which treat documents independently and some utilize inter-document similarities. Empirical evaluation shows that relevant documents that are centrally located within the similarity space of the relevant-documents set tend to be good representatives. In addition, we show that there exist highly representative clusters of similar relevant documents, and devise methods for ranking clusters based on their presumed representativeness. Finally, we study the connection between representativeness and TREC's gradual relevance judgments.
A Boron‐Based Synthesis of the Natural Product (+)‐<i>trans</i>‐Dihydrolycoricidine (2011)

Diastereoselective diboration results in the highly selective 1,4-dihydroxylation of chiral cyclohexadienes (see scheme). Together with the catalytic enantioselective conjugate allylboration, the diene diboration facilitates the asymmetric synthesis of the cytotoxic agent (+)-trans-dihydrolycoricidine (1). pin=pinacol. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Optical microphone for the detection of hidden helicopters (1992)

Analytical and experimental work demonstrate that an acoustic radiator impresses upon the atmosphere a fundamental frequency and harmonics that frequency shift the Doppler frequency resulting from the convective air motion. The net effect is the creation of a signature that depends on the acoustic pressure
An evaluation of automated homology modelling methods at low target–template sequence similarity (2007)

When using Modeller as the common modelling program, 3D-Coffee outperforms Staccato and SAlign using both multiple templates and the best single template, and across the sequence identity range 20-50%. The mean model RMSD generated from 3D-Coffee using multiple templates is 15 and 28% (or using single templates, 3 and 13%) better than those generated by Staccato and Salign, respectively. 3D-Coffee gives equivalent modelling accuracy from multiple and single templates, but Staccato and SAlign are more successful with single templates, their quality deteriorating as additional lower sequence identity templates are added. Evaluating the different homology modelling programs, on average Modeller performs marginally better in overall modelling than the others tested. However, on average Nest produces the best loops with an 8% improvement by mean RMSD compared to the loops generated by Builder.