gebhart/patrepeval huggingface dataset:
<title>Clear-channel strategies for a scalable wide-area network</title> (1995)

This paper studies the use of wavelength translation in different Clear Channel setup strategies in a scalable all-optical network. the network considered used a recursive grid architecture representing the 100 largest cities and constituting 561 access stations. As the network grows, the grid is subdivided in a recursive fashion to accommodate more nodes, making the network modular. The algorithm used for routing of the calls is distributed, dynamic, and scalable in the sense that the complexity of the algorithm grows slower than linear with the network size. The performance of wavelength translation with static and dynamic routing strategies is studied using simulation in terms of the blocking of incoming requests for Clear Channels. Optical wavelength translation is provided in the network and it is shown that for the network considered, the improvement in performance is marginal. The Clear Channel blocking, with and without wavelength translation, is studied for different traffic patterns ranging from fully uniform traffic to a pattern exhibiting very strong communities of interest. The impact of wavelength translation is considered for these different traffic patters. The Clear Channel setup strategies along with the architecture are all scalable and hence are applicable to very large networks.
Statistical analysis of the UWB channel in an industrial environment (2005)

In this paper, we present a statistical model for the ultra-wideband (UWB) channel in an industrial environment. Based on a set of measurements in a factory hall, we find that the abundance of metallic scatterers causes dense multipath scattering. This can be seen to produce mostly a Rayleigh distributed small-scale fading signal, with only a few paths exhibiting Nakagami distributions. For the power delay profile, we suggest a generalization of the Saleh-Valenzuela model where clusters with different excess delays have different ray power decay constants; the decay constants follow a linear dependence on the delay. This model provides an excellent fit to the measured data. We also note that for non-line-of-sight scenarios at larger distances, several hundred multipath components need to be collected to capture 50% of the available energy.
Wetting morphologies at microstructured surfaces (2005)

The wetting of microstructured surfaces is studied both experimentally and theoretically. Even relatively simple surface topographies such as grooves with rectangular cross section exhibit a large variety of different wetting morphologies as observed by atomic force microscopy. This polymorphism arises from liquid wedge formation along the groove corners and from contact line pinning along the groove edges. A global morphology diagram is derived that depends only on two system parameters: (i) the aspect ratio of the groove geometry and (ii) The contact angle of the underlying substrate material. For microfluidics, the most interesting shape regimes involve extended liquid filaments, which can grow and shrink in length while their cross section stays essentially constant. Thus, any method by which one can vary the contact angle can be used to switch the length of the filament, as is demonstrated in the context of electrowetting.
Dictionary of American business (2000)

The basic vocabulary used in most business situations as well as the special vocabulary of the stock exchange, conventions, accounting, and advertising are all included in this dictionary of American business terms. More than 11,000 terms are defined, each accompanied by a phonetic pronunciation guide, grammar notes, and sample sentences drawn from business publications. This is perfect for people who use English as a second language or for those who are studying or entering business for the first time. This replaces 0-948549-11-4.
Structural Requirements for Monoterpenoid Activity against Insects (1994)

The topical, fumigant and ovicidal activity of fourteen monoterpenoids and thirty-one monoterpenoid derivatives were evaluated using the house fly, Musca domestica. The toxicity data of acyclic, monocyclic, and tricyclic phenols, alcohols, and ketones were compared to determine structure-activity relationships involving the monoterpenoids' structural shape, type of functional group, and degree of saturation. Monoterpenoid acetate, propionate, pivalate, trichloroacetate, and trifluoroacetate derivatives were synthesized and their insecticidal activities were evaluated. The toxicities of the monoterpenoid acetate and haloacetate derivatives were compared with each other and the parent alcohols or phenols to evaluate the influence of derivatization on toxicity. Monoterpenoid ketones were more insecticidal than alcohols in the topical and ovicidal bioassays. Pivalate and acetate derivatives were more toxic than the haloacetate derivatives in both the topical and ovicidal bioassays. Thymyl trifluoroacetate was the most effective fumigant followed by menthol and fenchone. Thymol and geranyl acetate were the most insecticidal monoterpenoid and monoterpenoid derivative in the topical bioassays. Geraniol, geranyl propionate, terpineol, carvacrol and menthone were as ovicidal as the pyrethrin standard.
Probability of DNA knotting and the effective diameter of the DNA double helix. (1993)

During the random cyclization of long polymer chains, knots of different types are formed. We investigated experimentally the distribution of knot types produced by random cyclization of phage P4 DNA via its long cohesive ends. The simplest knots (trefoils) predominated, but more complex knots were also detected. The fraction of knots greatly diminished with decreasing solution Na+ concentration. By comparing these experimental results with computer simulations of knotting probability, we calculated the effective diameter of the DNA double helix. This important excluded-volume parameter is a measure of the electrostatic repulsion between segments of DNA molecules. The calculated effective DNA diameter is a sensitive function of electrolyte concentration and is several times larger than the geometric diameter in solutions of low monovalent cation concentration.
EML4-ALK Fusion Lung Cancer: A Rare Acquired Event (2008)

A recurrent gene fusion between EML4 and ALK in 6.7% of non-small cell lung cancers (NSCLCs) and NKX2-1 (TTF1, TITF1) high-level amplifications in 12% of adenocarcinomas of the lung were independently reported recently. Because the EML4-ALK fusion was only shown by a reverse transcription-polymerase chain reaction approach, we developed fluorescent in situ hybridization assays to interrogate more than 600 NSCLCs using break-apart probes for EML4 and ALK. We found that EML4-ALK fusions occur in less than 3% of NSCLC samples and that EML4 and/or ALK amplifications also occur. We also observed that, in most cases in which an EML4/ALK alteration is detected, not all of the tumor cells harbor the lesion. By using a detailed multi-fluorescent in situ hybridization probe assay and reverse transcription-polymerase chain reaction, we have evidence that other, more common mechanisms besides gene inversion exist including the possibility of other fusion partners for ALK and EML4. Furthermore, we confirmed the NKX2-1 high-level amplification in a significant subset of NSCLC and found this amplification to be mutually exclusive to ALK and EML4 rearrangements.
Genetics of digalactoside-binding adhesin from a uropathogenic Escherichia coli strain (1983)

The uropathogenic strain Escherichia coli J96 mediates mannose-resistant hemagglutination owing to production of a digalactoside-binding adhesin. A cosmid clone from this strain has been isolated that, when harbored in E. coli K-12, expressed Pap pili and this adhesin (R. Hull et al., Infect. Immun. 33:933-938, 1981). By transposon mutagenesis and by the construction of a number of hybrid plasmid derivatives, we have demonstrated that about 8.5 kilobases of DNA is required to generate a mannose-resistant hemagglutination-positive phenotype in E. coli K-12 strain P678-54. The structural gene for the Pap pili monomer, papA, has been identified and mapped close to the promotor-proximal end of the Pap operon. Although strain P678-54 that harbored a Tn5 insertion within papA showed a mannose-resistant hemagglutination-positive phenotype, it was negative in a competitive enzyme-linked immunosorbent assay with anti-Pap pilus serum. This could mean that a Pap adhesin is encoded by a region on the Pap operon that is distinct from papA.
High-speed, high-reliability circuit design for megabit DRAM (1991)

Circuit techniques for improving the speed and reliability of submicrometer geometry CMOS DRAMs are described. Double-bootstrap voltages are eliminated with an internal voltage supply and a unique word-line driver, reducing stress on short-channel devices. A row and column redundancy technique equivalent to physical disconnect of word lines and bit lines solves leakage problems. Speed enhancements are achieved through bit-line isolation for accelerated column access, a high-speed SRAM-style data path, and by tailoring sensing currents within the limitations of package inductance. The design of a fast 1-Mb DRAM employing these circuits is outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Involvement of intracellular Ca2+ in oxidant‐induced NF‐κB activation (1996)

In human Jurkat T cells and its subclone Wurzburg cells oxidant challenge elevated [Ca2+]i by mobilizing Ca2+ from intracellular stores. In Jurkat cells this effect was rapid and transient, but in Wurzburg cells the response was slow and sustained. H2O2-induced NF-kappaB activation in Wurzburg cells was not influenced by the presence of extracellular EGTA but was totally inhibited in cells that were loaded with esterified EGTA. In Jurkat cells that are not sensitive to H2O2-induced NF-kappaB activation, H2O2 potentiated NF-kappaB activation in the presence of sustained high [Ca2+]i following thapsigargin treatment. NF-kappaB regulatory effect of alpha-lipoate and N-acetylcysteine appeared to be, at least in part, due to their ability to stabilize elevation of [Ca2+]i following oxidant challenge. Results of this study indicate that a sustained elevated [Ca2+]i is a significant factor in oxidant-induced NF-kappaB activation.
Fetal to adult hemopoietic cell transplantation in humans: insights into hemoglobin switching (1986)

Abstract A 2-year-old boy with refractory acute leukemia (ALL) was transplanted with liver cells from twin fetuses of an 18-gestational-week age. Regeneration of hemopoietic cells was evident during the second week following transplantation when a cellular, predominantly erythroid, marrow was present. Studies of bone marrow and peripheral blood cells obtained 21 days posttransplant showed that bone marrow and peripheral blood BFU-E-derived erythroblasts displayed typical fetal patterns of globin chain synthesis (gamma/gamma + beta ratios: 0.87 to 0.98). In addition, all of the individually analyzed erythroid clones displayed a fetal type of globin program, suggesting that the presence of rare, partially switched clones was unlikely. Additional evidence supported the fetal phenotype of these progenitors. The il expression of culture- derived erythroblasts was typical for fetal erythroid cells. As in fetal cells, fetal sheep serum influenced neither the globin nor the il phenotypes, and the growth characteristics were as those observed in fetal liver cultures. That these fetal progenitors matured in vivo and produced cells with a fetal program was shown by the pattern of globin biosynthesis in bone marrow cells and peripheral blood reticulocytes (gamma/gamma + beta ratios: 0.85 to 0.95) at days 14 and 21 posttransplantation. These results indicate that the transplanted fetal cells, in spite of their proliferation and differentiation in the environment of the recipient, continued to express during the early posttransplantation period fetal patterns of globin, surface antigenic determinants, and growth and response to environmental modulation. The observations in this patient support the notion that hemoglobin switching is primarily controlled by a mechanism intrinsic to the stem cell.
cAMP and ras signalling independently control spore germination in the filamentous fungus Aspergillus nidulans (2002)

The role of cAMP signalling during germination of asexual spores (conidia) of the filamentous fungus Aspergillus nidulans was investigated. A. nidulans strains defective for adenylate cyclase (CyaA) or for the functionally overlapping cAMP-dependent protein kinase (PkaA) and newly characterized SchA protein kinase, homologous to Saccharomyces cerevisiae Sch9, show altered trehalose mobilization and kinetics of germ tube outgrowth, in addition to other defects in colony formation. cAMP-dependent trehalose breakdown is triggered by the addition of a carbon source independently of further catabolism, suggesting that cAMP signalling controls early events of conidial germination in response to carbon source sensing. Additional results suggest that cAMP has targets other than PkaA and SchA and that PkaA retains activity in the absence of cAMP. Conversely, PkaA regulates cAMP levels in A. nidulans because these are elevated by approximately 250-fold in a strain that lacks PkaA. Furthermore, analysis of mutant strains impaired in both adenylate cyclase and RasA GTPase previously implicated in the control of A. nidulans spore germination suggested that RasA and cAMP signalling proceed independently during germination in A. nidulans.
Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing (2021)

Profiling diverse microbiomes is revolutionizing our understanding of biological mechanisms and ecologically relevant problems, including metaorganism (host + microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci has therefore become an instrumental tool for many researchers. Investigations in many systems are hindered, however, since essential sequencing depth can be lost by amplification of nontarget DNA from hosts or overabundant microorganisms. Here, we introduce "blocking oligos", a low-cost and flexible method using standard oligonucleotides to block amplification of diverse nontargets and software to aid their design. We apply them primarily in leaves, where exceptional challenges with host amplification prevail. A. thaliana-specific blocking oligos applied in eight different target loci reduce undesirable host amplification by up to 90%. To expand applicability, we designed universal 16S and 18S rRNA gene plant blocking oligos for targets that are conserved in diverse plant species and demonstrate that they efficiently block five plant species from five orders spanning monocots and dicots (Bromus erectus, Plantago lanceolata, Lotus corniculatus, Amaranth sp., Arabidopsis thaliana). These can increase alpha diversity discovery without biasing beta diversity patterns and do not compromise microbial load information inherent to plant-derived 16S rRNA gene amplicon sequencing data. Finally, we designed and tested blocking oligos to avoid amplification of 18S rRNA genes of a sporulating oomycete pathogen, demonstrating their effectiveness in applications well beyond plants. Using these tools, we generated a survey of the A. thaliana leaf microbiome based on eight loci targeting bacterial, fungal, oomycete and other eukaryotic microorganisms and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. This approach has potential to make questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems-based insights into microbial discovery. For fast and easy design for blocking oligos for any nontarget DNA in other study systems, we developed a publicly available R package.
A d‐antifreeze polypeptide displays the same activity as its natural l‐enantiomer (1993)

The D- and L-forms of an alpha-helical antifreeze polypeptide (AFP) have been chemically synthesized. Circular dichroism spectra of the molecules show equal and opposite ellipticites. The D- and the L-enantiomers alone, and a 50:50 mixture of the two, all show identical antifreeze activity, but the enantiomeric forms are predicted to bind to the ice surface with different orientations. It is suggested that symmetry properties of certain ice surfaces permit the asymmetric binding of AFPs, and thus that AFPs are analogous to enzymes that act upon prochiral substrates.
Comparative Structural Analysis and Kinetic Properties of Lactate Dehydrogenases from the Four Species of Human Malarial Parasites (2004)

Parasite lactate dehydrogenase (pLDH) is a potential drug target for new antimalarials owing to parasite dependence on glycolysis for ATP production. The pLDH from all four species of human malarial parasites were cloned, expressed, and analyzed for structural and kinetic properties that might be exploited for drug development. pLDH from Plasmodium vivax, malariae, and ovale exhibit 90-92% identity to pLDH from Plasmodium falciparum. Catalytic residues are identical. Resides I250 and T246, conserved in most LDH, are replaced by proline in all pLDH. The pLDH contain the same five-amino acid insert (DKEWN) in the substrate specificity loops. Within the cofactor site, pLDH from P. falciparum and P. malariae are identical, while pLDH from P. vivax and P. ovale have one substitution. Homology modeling of pLDH from P. vivax, ovale, and malariae with the crystal structure of pLDH from P. falciparum gave nearly identical structures. Nevertheless, the kinetic properties and sensitivities to inhibitors targeted to the cofactor binding site differ significantly. Michaelis constants for pyruvate and lactate differ 8-9-fold; Michaelis constants for NADH, NAD(+), and the NAD(+) analogue 3-acetylpyridine adenine dinucleotide differ up to 4-fold. Dissociation constants for the inhibitors differ up to 21-fold. Molecular docking studies of the binding of the inhibitors to the cofactor sites of all four pLDH predict similar orientations, with the docked ligands positioned at the nicotinamide end of the cofactor site. pH studies indicate that inhibitor binding is independent of pH in the pH 6-8 range, suggesting that differences in dissociation constants for a specific inhibitor are not due to altered active site pK values among the four pLDH.
Differential growth sensitivity to 4-cis-hydroxy-L-proline of transformed rodent cell lines. (1988)

The effect of 4-cis-hydroxy-L-proline (CHP), a proline analogue, on the anchorage-dependent and -independent growth of several transformed rodent cell lines was studied. Mouse NIH-3T3 fibroblasts transformed by a variety of different oncogenes (Ki-ras, mos, src, fms, fes, met, and trk) by a DNA tumor virus (SV40) or by a chemical carcinogen (N-methylnitrosourea) were all found to be more sensitive (50% inhibitory dose, 20 to 55 micrograms/ml) to the dose-dependent inhibitory effects of CHP on growth in monolayer culture than were NIH-3T3 cells (50% inhibitory dose, 120 micrograms/ml). CHP was generally found to be even more effective in inhibiting the growth of these transformed cells as colonies in soft agar than in monolayer cultures. In addition, rat embryo fibroblasts (CREF) and normal rat kidney fibroblasts (NRK) after transformation with a Ki-ras oncogene exhibit a similar increase in their sensitivity to CHP-induced growth inhibition. Treatment of NRK cells with transforming growth factor alpha (TGF-alpha) and beta (TGF-beta), which reversibly induces phenotypic transformation of these cells, increases their sensitivity to CHP to a level comparable with that observed in Ki-ras-transformed NRK cells (K-NRK). The growth inhibitory effects of CHP are reversible, since removal of CHP results in a normal resumption of cell growth. CHP uptake occurs primarily through the Na+- and energy-dependent neutral amino acid transport A system, which is 6- to 7-fold more elevated in K-NRK cells compared with NRK cells. Treatment of NRK cells with TGF-alpha and/or -beta increases the uptake of [3H]methylaminoisobutyric acid on the A system to a level that is similar to that found in K-NRK cells. The functions of the Na+/K+ and Na+/H+ exchange systems are apparently necessary for the enhanced A system activity, since ouabain and amiloride can inhibit the uptake of [3H]methylaminoisobutyric acid in K-NRK cells and in NRK cells treated with TGF-alpha and/or -beta. The activity of the A system is specifically increased in K-NRK and in TGF-alpha- and/or -beta-treated NRK cells, since the other two major neutral amino acid uptake systems, the ASC and the L systems, and the Ly+ system for basic amino acid uptake show no apparent changes in their activity in NRK cells after treatment with TGF-alpha and/or -beta or in these cells after transformation with the Ki-ras oncogene. These results suggest that the differential growth sensitivity to CHP of transformed rodent cells and of normal fibroblasts treated with TGF-alpha and/or -beta is due in part to an elevated uptake of this amino acid analogue on the neutral amino acid transport A system.
General base catalysis of ester hydrolysis (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneral base catalysis of ester hydrolysisDimitrios Stefanidis and William P. JencksCite this: J. Am. Chem. Soc. 1993, 115, 14, 6045–6050Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/ja00067a020https://doi.org/10.1021/ja00067a020research-articleACS PublicationsRequest reuse permissionsArticle Views3518Altmetric-Citations69LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating (2006)

Gold nanoparticles appear to be superior handles in optical trapping assays. We demonstrate that relatively large gold particles (R(b)=50 nm) indeed yield a sixfold enhancement in trapping efficiency and detection sensitivity as compared to similar-sized polystyrene particles. However, optical absorption by gold at the most common trapping wavelength (1064 nm) induces dramatic heating (266 degrees C/W). We determined this heating by comparing trap stiffness from three different methods in conjunction with detailed modeling. Due to this heating, gold nanoparticles are not useful for temperature-sensitive optical-trapping experiments, but may serve as local molecular heaters. Also, such particles, with their increased detection sensitivity, make excellent probes for certain zero-force biophysical assays.