gebhart/patrepeval huggingface dataset:
Expression of a complete soybean leghemoglobin gene in root nodules of transgenic Lotus corniculatus (1987)

The complete soybean leghemoglobin lbc(3) gene was transferred into the legume Lotus corniculatus using an Agrobacterium rhizogenes vector system. Organ-specific expression of the soybean gene was observed in root nodules formed on regenerated transgenic plants after infection with Rhizobium loti. The primary transcript was processed in the same way as in soybean nodules and the resulting mRNA was translated into Lbc(3) protein. Quantitative determination of the Lbc(3) protein in nodules of transgenic plants indicated that the steady-state level of the soybean protein is comparable to that of endogenous Lotus leghemoglobin.
Peptide−Nanowire Hybrid Materials for Selective Sensing of Small Molecules (2008)

The development of a miniaturized sensing platform for the selective detection of chemical odorants could stimulate exciting scientific and technological opportunities. Oligopeptides are robust substrates for the selective recognition of a variety of chemical and biological species. Likewise, semiconducting nanowires are extremely sensitive gas sensors. Here we explore the possibilities and chemistries of linking peptides to silicon nanowire sensors for the selective detection of small molecules. The silica surface of the nanowires is passivated with peptides using amide coupling chemistry. The peptide/nanowire sensors can be designed, through the peptide sequence, to exhibit orthogonal responses to acetic acid and ammonia vapors, and can detect traces of these gases from "chemically camouflaged" mixtures. Through both theory and experiment, we find that this sensing selectivity arises from both acid/base reactivity and from molecular structure. These results provide a model platform for what can be achieved in terms of selective and sensitive "electronic noses."
Design, Fabrication, and Characterization of Thermally Actuated Probe Arrays for Dip Pen Nanolithography (2004)

In Dip Pen Nanolithography (DPN), arbitrary nanoscale chemical patterns can be created by the diffusion of chemicals from the tip of an atomic force microscope (AFM) probe to a surface. This paper describes the design, optimization, fabrication, and testing of an actuated multi-probe DPN array. The probe array consists of 10 thermal bimorph active probes made of silicon nitride and gold. The probes are 300 /spl mu/m long and the tips are spaced 100 /spl mu/m apart. An actuation current of 10 mA produces a tip deflection of 8 /spl mu/m, which is enough to remove individual tips from the surface independent of the adjacent probes. An analytical probe model is presented and used to optimize the design against several possible failure modes. The array is demonstrated by using it to simultaneously write 10 unique octadecanethiol patterns on a gold surface. Pattern linewidth as small as 80 nm has been created at a maximum write speed of 20 /spl mu/m/sec. By writing multiple, distinctly different patterns in parallel, this device provides a significant improvement in throughput and flexibility over conventional AFM probes in the DPN process.
Direct removal in the mouse of a floxed neo gene from a three‐loxp conditional knockout allele by two novel approaches (2001)

The presence in an intron of the ploxP-neo-loxP cassette often results in severe interference with gene expression. Consequently, many investigators selectively remove the ploxP-neo-loxP cassette by transient expression of Cre in ES cells. Although effective, the added manipulation of the ES cells may reduce the likelihood that a clone will be able to transmit via the germline. Therefore, we developed two novel approaches that remove the ploxP-neo-loxP by Cre-mediated recombination in mouse. First, the ploxP-neo-loxP-containing mice were crossed with EIIa-Cre transgenic mice. Second, a Cre-expression plasmid was injected into pronuclei of fertilized eggs bearing the ploxP-neo-loxP allele. Both approaches produced mosaic mice with partial and complete excision. These mosaic mice were then mated, and the neo-less conditional knockout allele was found in the offspring after screening only a few litters. These procedures provide options for removing neo directly in the mouse in addition to the commonly used approach that deletes neo in ES cells.
Multiple endoglycosidase F activities expressed by Flavobacterium meningosepticum endoglycosidases F2 and F3. Molecular cloning, primary sequence, and enzyme expression (1993)

The genes for Flavobacterium meningosepticum Endo (endoglycosidase) F2 and Endo F3 were cloned, and their nucleotide sequences were determined. The deduced amino acid sequences were verified independently to a large extent by direct peptide microsequencing of 66 and 84% of native Endo F2 and Endo F3, respectively. Structurally, the Endo F2 and Endo F3 genes code for a typically long leader sequence of 45 and 39 amino acids, respectively, and, in both cases, a mature protein of 290 amino acids. Comparative structural analysis demonstrated minimum overall homology (15-30%) between Endo F1, Endo F2, and Endo F3, but revealed distinct clusters of identical residues distributed throughout the entire sequence, which represent motifs for binding and hydrolysis of beta 1,4-di-N-acetylchitobiosyl linkages in complex carbohydrates. The mobility of native Endo F2 and Endo F3 on SDS-polyacrylamide gel electrophoresis, unlike Endo F1, did not correlate with the molecular weights determined from the coding region of the corresponding genes. Mass spectrometry confirmed that Endo F2 and Endo F3 were heterogeneous and contained approximately 4000 and 1200 daltons of mass not accounted for in the gene structure. We presume that Endo F2 and Endo F3 are variably post-translationally modified during secretion by possible linkage to the hydroxyl of serine.
Detection of organic vapors with active and passive sensors: a comparison (1986)

Many organic compounds of medium complexity have their most characteristic spectral features in the 8–12-μm region of the IR. Both active and passive sensors can be used for detection of these compounds. The active systems are based on pulsed CO2 lasers and direct detection sensors operated in either the distributed (range resolved) or topographic reflector modes. Passive sensors are based on natural temperature differences which exist between the background and target cloud. The effects of throughput, collecting aperture size, electronic bandwidth, background noise, speckle noise, laser energy, and temperature difference are discussed for active and passive spectral sensors. The noise equivalent concentration path length product is used to define performance for both passive and active sensors. The computed results are compared to recently published reports.
The Structure of Terramycin1,2 (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Structure of Terramycin1,2F. A. Hochstein, C. R. Stephens, L. H. Conover, P. P. Regna, R. Pasternack, P. N. Gordon, F. J. Pilgrim, K. J. Brunings, and R. B. WoodwardCite this: J. Am. Chem. Soc. 1953, 75, 22, 5455–5475Publication Date (Print):November 1, 1953Publication History Published online1 May 2002Published inissue 1 November 1953https://pubs.acs.org/doi/10.1021/ja01118a001https://doi.org/10.1021/ja01118a001research-articleACS PublicationsRequest reuse permissionsArticle Views949Altmetric-Citations147LEARN 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
Differences in Antibiotic Resistance Patterns ofEnterococcus faecalisandEnterococcus faeciumStrains Isolated from Farm and Pet Animals (2001)

The prevalence of acquired resistance in 146 Enterococcus faecium and 166 Enterococcus faecalis strains from farm and pet animals, isolated in 1998 and 1999 in Belgium, against antibiotics used for growth promotion and for therapy was determined. Acquired resistance against flavomycin and monensin, two antibiotics used solely for growth promotion, was not detected. Avoparcin (glycopeptide) resistance was found sporadically in E. faecium only. Avilamycin resistance was almost exclusively seen in strains from farm animals. Resistance rates were higher in E. faecium strains from broiler chickens than in strains from other animal groups with tylosin and virginiamycin and in E. faecalis as well as in E. faecium strains with narasin and bacitracin. Resistance against ampicillin was mainly found among E. faecium strains from pets and was absent in E. faecalis. Tetracycline resistance occurred most often in strains from farm animals, while enrofloxacin resistance, only found in E. faecalis, occurred equally among strains from all origins. Resistance against gentamicin was very rare in broiler strains, whereas resistance rates were high in strains from other origins. It can be concluded that resistance against antibiotics used solely for growth promotion was more prevalent in E. faecium strains than in E. faecalis strains. With few exceptions, resistance against the different categories of antibiotics was more prevalent in strains from farm animals than in those from pets.
Thrombopoietin production by human embryonic kidney cells in culture. (1975)

Human embryonic kidney cells were maintained in culture in a medium containing lactalbumin hydrolysate for 5 to 6 weeks and the supernatant fluid tested for thrombopoietin content. Thrombopoietin was determined by a bioassay procedure which utilized mice that were in rebound thrombocytosis. The results indicate that the medium from kidney cells in culture contained a factor that stimulates thrombopoiesis in assay mice as measured by per cent 35-S incorporation into platelets. A dose-response relationship was demonstrated between the volume of thrombopoietically active production medium injected and the level of isotope that subsequently appeared in the circulating platelets. Thrombopoietin was not found in control production media. Moreover, thrombopoietin-rich production medium did not contain erythropoietin, erythroginin, or white blood cell-stimulating factors. The results of this study indicate that kidney cells in culture produce a specific thrombopoietic stimulating factor. It seems probable from these in virto data that a site of production of thrombopoietin in vivo is the kidney.
Efficient parallel set-similarity joins using MapReduce (2010)

In this paper we study how to efficiently perform set-similarity joins in parallel using the popular MapReduce framework. We propose a 3-stage approach for end-to-end set-similarity joins. We take as input a set of records and output a set of joined records based on a set-similarity condition. We efficiently partition the data across nodes in order to balance the workload and minimize the need for replication. We study both self-join and R-S join cases, and show how to carefully control the amount of data kept in main memory on each node. We also propose solutions for the case where, even if we use the most fine-grained partitioning, the data still does not fit in the main memory of a node. We report results from extensive experiments on real datasets, synthetically increased in size, to evaluate the speedup and scaleup properties of the proposed algorithms using Hadoop.
Development of cell‐free protein synthesis platforms for disulfide bonded proteins (2007)

The use of cell-free protein synthesis (CFPS) for recombinant protein production is emerging as an important technology. For example, the openness of the cell-free system allows control of the reaction environment to promote folding of disulfide bonded proteins in a rapid and economically feasible format. These advantages make cell-free protein expression systems particularly well suited for producing patient specific therapeutic vaccines or antidotes in response to threats from natural and man-made biological agents and for pharmaceutical proteins that are difficult to produce in living cells. In this work we assess the versatility of modern cell-free methods, optimize expression and folding parameters, and highlight the importance of rationally designed plasmid templates for producing mammalian secreted proteins, fusion proteins, and antibody fragments in our E. coli-based CFPS system. Two unique CFPS platforms were established by developing standardized extract preparation protocols and generic cell-free reaction conditions. Generic reaction conditions enabled all proteins to express well with the best therapeutic protein yield at 710 microg/mL, an antibody fragment at 230 microg/mL, and a vaccine fusion protein at 300 microg/mL; with the majority correctly folded. Better yields were obtained when cell-free reaction conditions were optimized for each protein. Establishing general CFPS platforms enhances the potential for cell-free protein synthesis to reliably produce complex protein products at low production and capital costs with very rapid process development timelines.
Phase I and phase IV strains of Bordetella pertussis carry a repeated DNA sequence not found in other Bordetella species* (1987)

Two phase I strains of Bordetella pertussis and their phase IV derivatives were shown to have a repeated DNA sequence. Differences in the pattern of hybridisation of this sequence to the phase I and phase IV strains were observed, suggesting that DNA rearrangements may have occurred. The repeated DNA sequence was not found in 3 strains each of B. parapertussis, B. bronchiseptica or B. avium.
Formation of Light-Guiding Interconnections in an Integrated Optical Circuit by Composite Tapered-Film Coupling (1973)

We demonstrate a new and simple method of forming light-guiding interconnections in an integrated optical circuit. This involves bridging the devices with a thin film having tapered ends that form naturally during the deposition process. Experiments show that there is no specific requirement for the thickness, refractive index, or relative position of the bridging film. A theory of composite waveguides provides an understanding of these interconnections.
Combinatorial Selection and Binding of Phosphorothioate Aptamers Targeting Human NF-κB RelA(p65) and p50 (2002)

Previously, we reported the in vitro combinatorial selection of phosphorothioate aptamers or "thioaptamers" targeting the transcription factor NF-IL6. Using the same approach and purified recombinant human NF-kappa B proteins RelA(p65) and p50, duplex thioaptamers have been selected that demonstrate high-affinity, competitive binding with the duplex 22-mer binding site, Ig kappa B. Binding energetics of RelA(p65) and p50 homodimers were studied using a quantitative electrophoretic mobility shift assay or EMSA. As a reference system for competitive aptamer binding, the duplex 22-mer phosphoryl binding site known as Ig kappa was determined to bind each p65 and p50 homodimer with a 1:1 stoichiometry and with affinities, determined by global analysis, K(d) = 4.8 +/- 0.2 nM for p65 and K(d) = 0.8 +/- 0.2 nM for p50. A global analysis tool for competitive NF-kappa B/Ig kappa binding was developed and utilized to measure the affinity of thioaptamers selected by both p65 and p50. The competition results indicate that the thioaptamers bind and compete for the same NF-kappa B site as the known promoter element Ig kappa B (K(d) = 78.9 +/- 1.9 nM for a p65-selected aptamer and 19.6 +/- 1.3 nM for a p50-selected thioaptamer). Qualitative gel shift binding experiments with p50 also demonstrate that the nature of enhanced affinity and specificity can be attributed to the presence of sulfur. Collectively, these results demonstrate the feasibility of the thioaptamer in vitro combinatorial selection technology as a method for producing specific, high-affinity ligands to proteins.
Upregulation of the Genes Encoding Lysosomal Hydrolases, a Perforin-Like Protein, and Peroxidases in the Brains of Mice Affected with an Experimental Prion Disease (2000)

In an attempt to identify the molecules involved in the pathogenesis of prion diseases, we performed cDNA subtraction on the brain tissues of mice affected with an experimental prion disease and the unaffected control. The genes identified as being upregulated in the prion-affected brain tissue included those encoding a series of lysosomal hydrolases (lysozyme M and both isoforms of beta-N-acetylhexosaminidase), a perforin-like protein (macrophage proliferation-specific gene-1 [MPS-1]), and an oxygen radical scavenger (peroxiredoxin). Dramatic increases in the expression level occurred at between 12 and 16 weeks after intracerebral inoculation of the prion, coinciding with the onset of spongiform degeneration. The proteinase K-resistant prion protein (PrP(Sc)) became detectable by immunoblotting well before 12 weeks, suggesting a causal relationship between this and the gene activation. Immunohistochemistry paired with in situ hybridization on sections of the affected brain tissue revealed that expression of the peroxiredoxin gene was detectable only in astrocytes and was noted throughout the affected brain tissue. On the other hand, the genes for the lysosomal hydrolases and MPS-1 were overexpressed exclusively by microglia, which colocalized with the spongiform morphological changes. A crucial role for microglia in the spongiform degeneration by their production of neurotoxic substances, and possibly via the aberrant activation of the lysosomal system, would have to be considered.
Integrating Image-Based High-Content Screening with Mouse Models Identifies 5-Hydroxydecanoate as a Neuroprotective Drug for Paclitaxel-Induced Neuropathy (2015)

Chemotherapy-induced neurotoxicity is a common adverse effect of cancer treatment. No medication has been shown to be effective in the prevention or treatment of chemotherapy-induced neurotoxicity. This study aimed to discover potential neuroprotective drugs for paclitaxel-induced neurotoxicity. An image-based high-content platform was first developed to screen for potential neuroprotective drugs. The screening system comprised of automated image acquisition and multiparameter analysis, including neuronal viability, neurite outgrowth, and synaptogenesis. By this platform, we obtained a candidate list from compound libraries. In the drug screening from compound libraries of ion channel ligands, REDOX and GABAergic ligands, 5-hydroxydecanoate (5-HD) exhibited the most significant neuroprotective effects against paclitaxel-induced neurotoxicity in both cortical and dorsal root ganglion (DRG) neurons. In mouse behavioral tests, 5-HD restored the thermal sensitivity and alleviated mechanical allodynia induced by paclitaxel. Electron micrographs of sciatic nerve revealed that 5-HD reduced the damages caused by paclitaxel in the nonmyelinated and smaller myelinated fibers. The mechanistic study on DRG neurons suggested that 5-HD rescued the dysregulation of intracellular calcium homeostasis provoked by paclitaxel. Importantly, 5-HD did not jeopardize the antitumor effect of paclitaxel in tumor xenograft models. In conclusion, we established an imaged-based high-content screening platform and a protocol for verifying the neuroprotective effect in vivo, by which 5-HD was identified and validated as a potential neuroprotective drug for paclitaxel-induced neuropathy.
Heterogeneity of human blood monocyte: two subpopulations with different sizes, phenotypes and functions. (1992)

Human blood mononuclear cells from normal adults were collected after density-cut centrifugation and monocytes were then isolated by removal of lymphocytes using the techniques of E-rosetting and cell adhesion. The purified monocytes were further analysed by velocity sedimentation, and two distinct subpopulations with different cell sizes were obtained. The larger monocytes were 17.0 +/- 1.8 microns in diameter with a mean sedimentation rate (SR) of 7.0 +/- 0.6 mm/hr, while the smaller monocytes were 9.5 +/- 0.8 microns in size and 4.1 +/- 0.2 mm/hr in SR. The population ratio of larger:smaller cells was approximately 2:1 (66 +/- 2.8%:34 +/- 1.6%). Both cell populations exhibited a high positive rate (> 98%) in both the non-specific esterase and the peroxidase stain. However, the larger cells had much higher phagocytic activity than the smaller ones. Furthermore, the expression of monocyte-associated antigens was also different between these two subpopulations. Thus, while most of the larger monocytes (98%) could be recognized by monoclonal antibodies MY7 and OKM1, only some (35 and 61%, respectively) of the smaller monocytes could react with those antibodies. In addition, the larger monocytes secreted a significant amount of monokines including interleukin-1 beta (IL-1 beta), tumour necrosis factor-alpha (TNF-alpha) and prostaglandin E2 (PGE2) and their production increased in proportion to the level of stimulation by bacterial lipopolysaccharide (LPS), whereas the production of monokines by the smaller monocytes remained at low levels and did not respond to LPS stimulation. These results reveal the existence of phenotypic and functional heterogeneity in human blood monocytes.
The Munich 2011 CHiME Challenge Contribution: NMF-BLSTM Speech Enhancement and Recognition for Reverberated Multisource Environments (2011)

We present the Munich contribution to the PASCAL 'CHiME' Speech Separation and Recognition Challenge: Our approach combines source separation by supervised convolutive non-negative matrix factorisation (NMF) with our tandem recogniser that augments acoustic features by word predictions of a Long Short-Term Memory recurrent neural network in a multi-stream Hidden Markov Model.The performance of our source separation approach is demonstrated in a sequence of gradually refined speech recognisers.While NMF drastically improves performance for all investigated recognisers, best results are obtained with the multi-stream approach along with a novel adaptation technique for noise dictionaries in supervised NMF.On the final Challenge test set, the proposed system delivers an average keyword recognition accuracy of 87.86 % across SNRs ranging from -6 to 9 dB, reducing the error rate from 44 % to 12 % compared to the Challenge baseline.