gebhart/patrepeval huggingface dataset:
Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce (2012)

The presence, size and importance of bacterial communities on plant leaf surfaces are widely appreciated. However, information is scarce regarding their composition and how it changes along geographical and seasonal scales. We collected 106 samples of field-grown Romaine lettuce from commercial production regions in California and Arizona during the 2009-2010 crop cycle. Total bacterial populations averaged between 10(5) and 10(6) per gram of tissue, whereas counts of culturable bacteria were on average one (summer season) or two (winter season) orders of magnitude lower. Pyrosequencing of 16S rRNA gene amplicons from 88 samples revealed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria were the most abundantly represented phyla. At the genus level, Pseudomonas, Bacillus, Massilia, Arthrobacter and Pantoea were the most consistently found across samples, suggesting that they form the bacterial 'core' phyllosphere microbiota on lettuce. The foliar presence of Xanthomonas campestris pv. vitians, which is the causal agent of bacterial leaf spot of lettuce, correlated positively with the relative representation of bacteria from the genus Alkanindiges, but negatively with Bacillus, Erwinia and Pantoea. Summer samples showed an overrepresentation of Enterobacteriaceae sequences and culturable coliforms compared with winter samples. The distance between fields or the timing of a dust storm, but not Romaine cultivar, explained differences in bacterial community composition between several of the fields sampled. As one of the largest surveys of leaf surface microbiology, this study offers new insights into the extent and underlying causes of variability in bacterial community composition on plant leaves as a function of time, space and environment.
Identification of functional murine adenosine deaminase cDNA clones by complementation in Escherichia coli. (1985)

Total poly(A+) RNA derived from a mouse cell line with amplified adenosine deaminase genes was used as template to synthesize double-stranded cDNA. The cDNAs were inserted into the PstI site of the beta-lactamase gene in plasmid pBR322 following G-C tailing. After transformation into adenosine deaminase-deficient Escherichia coli hosts, recombinant plasmids containing functional murine adenosine deaminase cDNAs were identified by selecting for functional complementation. Analysis of plasmids containing functional adenosine deaminase cDNA sequences strongly suggested that adenosine deaminase expression resulted mainly from beta-lactamase/adenosine deaminase fusion proteins even when the adenosine deaminase codons were out-of-frame with respect to the beta-lactamase gene codons upstream. The nucleotide sequence of a 1.65-kilobase pair cDNA insert in one of the functional recombinant clones was determined and found to contain a 1056-nucleotide open reading frame. When this 1056-nucleotide open reading frame was inserted into a mammalian expression vector and introduced into monkey kidney cells, a high level of authentic mouse adenosine deaminase was produced. Nucleic acid blot analysis using a full-length adenosine deaminase cDNA clone as probe revealed that the mouse adenosine deaminase structural gene was at least 21 kilobase pairs in size and encoded three polyadenylated mRNAs. Analysis of the cDNA library from which the functional clones were isolated suggested that this approach of cloning functional mammalian adenosine deaminase cDNA clones by genetic complementation of enzyme-deficient bacteria could be accomplished even if the abundance of the adenosine deaminase mRNA sequences were as low as approximately 0.001%.
Antibacterial Activity of Conjugated Polyelectrolytes with Variable Chain Lengths (2011)

Cationic poly(phenylene ethynylene)- (PPE-) based conjugated polyelectrolytes (CPEs) with six different chain lengths ranging in degree of polymerization from ∼7 to ∼49 were synthesized from organic-soluble precursor polymers. The molecular weight of the precursor polymers was controlled by the amount of a monofunctional "end-capping" agent added to the polymerization reaction. Cationic CPEs were prepared by quaternization of amine groups to tetraalkylammonium groups. Their structure-property relationships were investigated by observing their photophysical properties and antibacterial activity. The polymers were found to exhibit a chain-length dependence in their photophysical properties. It has also been observed that the polymers exhibit effective antibacterial activity against both Gram-positive and Gram-negative bacteria under UV irradiation, whereas they show little antibacterial activity in the dark. An effect of chain length on the light-activated antibacterial activity was also found: The shortest polymer (n=7) exhibited the most effective antibacterial activity against both Gram-positive and Gram-negative bacteria.
Membrane‐tethered proteins for basic research, imaging, and therapy (2008)

Secreted and intracellular proteins including antibodies, cytokines, major histocompatibility complex molecules, antigens, and enzymes can be redirected to and anchored on the surface of mammalian cells to reveal novel functions and properties such as reducing systemic toxicity, altering the in vivo distribution of drugs and extending the range of useful drugs, creating novel, specific signaling receptors and reshaping protein immunogenicity. The present review highlights progress in designing vectors to target and retain chimeric proteins on the surface of mammalian cells. Comparison of chimeric proteins indicates that selection of the proper cytoplasmic domain and introduction of oligiosaccharides near the cell surface can dramatically enhance surface expression, especially for single-chain antibodies. We also describe progress and limitations of employing surface-tethered proteins for preferential activation of prodrugs at cancer cells, imaging gene expression in living animals, performing high-throughput screening, selectively activating immune cells in tumors, producing new adhesion molecules, creating local immune privileged sites, limiting the distribution of soluble factors such as cytokines, and enhancing polypeptide immunogenicity. Surface-anchored chimeric proteins represent a rich source for developing new techniques and creating novel therapeutics.
Electrospray ionization mass spectrometry of AZT <i>H</i>‐phosphonates conjugated with steroids (2003)

AZT H-phosphonates conjugated with steroids were synthesized and determined by positive and negative ion electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). The fragmentation pathways were investigated in detail. There are very different characteristic fragment ions in the positive and negative ion MS/MS spectra. The azide group of compounds 6a and 6b underwent either elimination of HN(3) or rearrangement to an amine in both positive and negative ion mass spectrometry.
Fast and long retention-time nano-crystal memory (1996)

A threshold-shifting, single transistor memory structure with fast read and write times and long retention time is described. The structure consists of a silicon field-effect transistor with nano-crystals of germanium or silicon placed in the gate oxide in close proximity of the inversion surface. Electron charge is stored in these isolated 2-5 nm size nano-crystals which are separated from each other by greater than 5 nm of SiO/sub 2/ and from the inversion layer of the substrate surface by less than 5 nm of SiO/sub 2/. Direct tunneling of charge from the inversion layer and its storage in the nano-crystal causes a shift in the threshold voltage which is detected via current sensing. The nano-crystals are formed using implantation and annealing or using direct deposition of the distributed floating gate region. Threshold shift of 0.3 V is obtained in Ge-implanted devices with 2 nm of SiO/sub 2/ injection layer by a 4 V write pulse of 300 ns duration. The nano-crystal memories achieve improved programming characteristics as a nonvolatile memory as well as simplicity of the single poly-Si-gate process. The V/sub T/ window is scarcely degraded after greater than 10/sup 9/ write/erase cycles or greater than 10/sup 5/ s retention time. Nano-crystal memories are promising for nonvolatile memory applications.
Objective Measurement of Perceived Auditory Quality in Multichannel Audio Compression Coding Systems (2008)

Objective quality assessment methods have been used widely for the evaluation of audio coding systems. However, even though many different competing multichannel audio compression coding systems are being developed, most current quality assessment methods only predict results for monaural or stereo signals. A prediction method is introduced that can be used for multichannel audio compression coding systems. The method introduces three variables as measures of the degradations in spatial quality: interaural time difference (ITD) distortion, interaural level difference (ILD) distortion, and interaural cross-correlation coefficient (IACC) distortion. Simultaneously ten model output variables proposed in ITU-R BS. 1387-1 are extracted from binaural signals that are synthesized using head-related transfer functions. The prediction model is trained and verified using results from subjective listening tests of multichannel audio compression coding systems that were performed by participants in the MPEG audio group. This new model, using the three interaural and ten nonspatial statistics, shows encouraging results in the prediction of perceived quality.
Glutaredoxins: Glutathione-Dependent Redox Enzymes with Functions Far Beyond a Simple Thioredoxin Backup System (2004)

Most cells contain high levels of glutathione and multiple glutaredoxins, which utilize the reducing power of glutathione to catalyze disulfide reductions in the presence of NADPH and glutathione reductase (the glutaredoxin system). Glutaredoxins, like thioredoxins, may operate as dithiol reductants and are involved as alternative pathways in cellular functions such as formation of deoxyribonucleotides for DNA synthesis (by reducing the essential enzyme ribonucleotide reductase), the generation of reduced sulfur (via 3'-phosphoadenylylsulfate reductase), signal transduction, and the defense against oxidative stress. The three dithiol glutaredoxins of E. coli with the active-site sequence CPYC and a glutathione binding site in a thioredoxin/glutaredoxin fold display surprisingly different properties. These include the inducible OxyR-regulated 10-kDa Grx1 or the highly abundant 24-kDa glutathione S-transferase-like Grx2 (with Grx3 it accounts for 1% of total protein). Glutaredoxins uniquely reduce mixed disulfides with glutathione via a monothiol mechanism where only an N-terminal low pKa Cys residue is required, by using their glutathione binding site. Glutaredoxins also catalyze formation of mixed disulfides (glutathionylation), which is an important redox regulatory mechanism, particularly in mammalian cells under oxidative stress conditions, to sense cellular redox potential.
Evaluation of the gene-specific dye bias in cDNA microarray experiments (2005)

http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique
Single-wall carbon nanotube networks as a transparent back contact in CdTe solar cells (2007)

Single-wall carbon nanotube (SWCNT) networks form a highly transparent and electrically conductive thin film that can be used to replace traditional transparent conducting oxides (TCOs) in a variety of applications. Here, the authors demonstrate their use as a transparent back contact in a near-infrared (NIR) transparent CdTe solar cell. SWCNT networks are hole-selective conductors and have a significantly greater NIR transparency than TCOs—qualities which could both make them very useful in tandem thin-film solar cells. SWCNT networks can be incorporated into single-junction CdTe devices and in CdTe top cells for mechanically stacked thin-film tandem devices, as described here. The best device efficiency using SWCNTs in the back contact was 12.4%, with 40%–50% transmission between 800 and 1500nm.
A novel conformationally restricted protein kinase C inhibitor, Ro 31‐8425, inhibits human neutrophil superoxide generation by soluble, particulate and post‐receptor stimuli (1991)

A novel, bis-indolylmaleimide, Ro 31-8425, bearing a conformationally restricted side chain, inhibits protein kinase C isolated from rat brain and human neutrophils with a high degree of selectivity over cAMP-dependent kinase and Ca2+/calmodulin-dependent kinase. It also inhibits phorbol ester-induced intracellular events known to be mediated by protein kinase C (p47 phosphorylation in intact platelets, CD3 and CD4 down-regulation in T-cells). Ro 31-8425 inhibited superoxide generation in human neutrophils activated by both receptor stimuli (formyl-methionyl-leucylphenylalanine, opsonized zymosan, IgG and heat aggregated IgG) and post-receptor stimuli (1,2-dioctanoylglycerol and fluoride). The compound also blocked antigen driven, but not IL-2 induced, T-cell proliferation. These results support a central role for protein kinase C in the activation of the respiratory burst and antigen-driven T-cell proliferation.
Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer's disease correlates with increased BACE1/β-secretase expression (2008)

Although the role of APP and PSEN genes in genetic Alzheimer's disease (AD) cases is well established, fairly little is known about the molecular mechanisms affecting Abeta generation in sporadic AD. Deficiency in Abeta clearance is certainly a possibility, but increased expression of proteins like APP or BACE1/beta-secretase may also be associated with the disease. We therefore investigated changes in microRNA (miRNA) expression profiles of sporadic AD patients and found that several miRNAs potentially involved in the regulation of APP and BACE1 expression appeared to be decreased in diseased brain. We show here that miR-29a, -29b-1, and -9 can regulate BACE1 expression in vitro. The miR-29a/b-1 cluster was significantly (and AD-dementia-specific) decreased in AD patients displaying abnormally high BACE1 protein. Similar correlations between expression of this cluster and BACE1 were found during brain development and in primary neuronal cultures. Finally, we provide evidence for a potential causal relationship between miR-29a/b-1 expression and Abeta generation in a cell culture model. We propose that loss of specific miRNAs can contribute to increased BACE1 and Abeta levels in sporadic AD.
Trigger inheritance and overriding in an active object database system (2000)

An active database is a database in which some operations are automatically executed when specified events happen and particular conditions are met. Several systems supporting active rules in an object oriented data model have been proposed. However, several issues related to the integration of triggers with object oriented modeling concepts have not been satisfactorily addressed. We discuss issues related to trigger inheritance and refinement in the context of the Chimera active object oriented data model. In particular, we introduce a semantics for an active object language that takes into account trigger inheritance and supports trigger overriding. Moreover, we state conditions on trigger overriding ensuring that trigger semantics is preserved in subclasses.
ChemInform Abstract: Ternary Halides of the A3MX6 Type. Part 7. The Bromides Li3LnBr6 (Ln: Sm‐Lu, Y): Synthesis, Crystal Structure, and Ionic Mobility. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Micromachined electrical field-flow fractionation (μ-EFFF) system (2002)

In this work, micromachining technologies are used in the development of the next generation of precision /spl mu/-EFFF separation systems. Current macromachining techniques are the limiting factor in the development of more effective Electrical Field-Flow Fractionation (EFFF) separation systems. EFFF systems are used to separate particles in colloids such as cells or proteins. In this paper, EFFF systems are compared to other separation systems and a review of past micromachining efforts in the area of separation systems is made. The theory behind the operation and resolution of an EFFF system is surveyed and the advantages to be gained from application of micromachining technologies are discussed. A method of fabrication that relies on micromachining technologies for /spl mu/-EFFF system construction is described. The /spl mu/-EFFF system setup is described, devices are tested, compared to the current macro EFFF systems, and the results reported.
Anti-inositolglycan antibodies selectively block some of the actions of insulin in intact BC3H1 cells. (1990)

We have studied the mechanism of generation of insulin mediators by using specific antibodies raised against the oligosaccharide anchor of membrane proteins. These antibodies (i) block the in vitro effects of purified insulin mediators and (ii) block the insulin-induced stimulation of pyruvate dehydrogenase in intact BC3H1 myocytes but not insulin-stimulated glucose uptake, generation of diacylglycerol, or generation of insulin mediators. When added to intact cells in the presence of insulin, these antibodies induce the accumulation of insulin mediator activity in the extracellular medium. We therefore conclude that these anti-inositolglycan antibodies block some of the effects of insulin by inhibiting the uptake of specific insulin mediators generated outside the cell.
Novel chromophoric heterocycles based on maleimide and naphthoquinone (1989)

Abstract 1‐Phenyl‐3,4‐dichloromaleimide, 1‐ n ‐propyl‐3‐bromomaleimide, and 2,3‐dichloro‐1,4‐naphthoquinone have been condensed with various mono‐ and bis‐nucleophiles to yield a range of novel dyes and pigments. Their visible absorption spectra are discussed.
Evidence That Dynorphin Plays a Major Role in Mediating Progesterone Negative Feedback on Gonadotropin-Releasing Hormone Neurons in Sheep (2004)

Endogenous opioid peptides (EOP) mediate progesterone-negative feedback in many species, but the specific EOP systems involved remain unresolved. We first addressed this question in sheep by determining the role of different EOP receptor subtypes in the medial basal hypothalamus (MBH) and preoptic area (POA). Local administration of EOP receptor antagonists to luteal phase ewes indicated that kappa-, but not micro- or delta-, receptors mediate the inhibition of LH secretion in the MBH. In contrast, both kappa- and micro-, but not delta-receptor, antagonists increased LH pulse frequency when placed in the POA. We next examined close appositions between dynorphin (kappa ligand) and beta-endorphin (micro ligand) containing varicosities and GnRH perikarya in luteal phase ewes using dual immunocytochemistry and light microscopy. Approximately 90% of MBH GnRH neurons had close associations by dynorphin-containing varicosities, but only 40-50% of GnRH perikarya elsewhere had such close associations. In contrast, the percentage of beta-endorphinergic varicosities close to GnRH neurons was similar among all regions. Electron microscopic analysis demonstrated both dynorphinergic synapses and beta-endorphinergic synapses onto GnRH perikarya. These and other data lead to the hypothesis that dynorphin neurons play a major role in progesterone-negative feedback in the ewe and that this inhibition may be exerted directly on GnRH perikarya within the MBH, whereas dynorphin and beta-endorphin input to GnRH neurons in the POA provide redundancy to this system or are involved in other actions of progesterone or estradiol in the control of the GnRH surge.
Ligand Redox Effects in the Synthesis, Electronic Structure, and Reactivity of an Alkyl−Alkyl Cross-Coupling Catalyst (2006)

The ability of the terpyridine ligand to stabilize alkyl complexes of nickel has been central in obtaining a fundamental understanding of the key processes involved in alkyl-alkyl cross-coupling reactions. Here, mechanistic studies using isotopically labeled (TMEDA)NiMe(2) (TMEDA = N,N,N',N'-tetramethylethylenediamine) have shown that an important catalyst in alkyl-alkyl cross-coupling reactions, (tpy')NiMe (2b, tpy' = 4,4',4' '-tri-tert-butylterpyridine), is not produced via a mechanism that involves the formation of methyl radicals. Instead, it is proposed that (terpyridine)NiMe complexes arise via a comproportionation reaction between a Ni(II)-dimethyl species and a Ni(0) fragment in solution upon addition of a terpyridine ligand to (TMEDA)NiMe(2). EPR and DFT studies on the paramagnetic (terpyridine)NiMe (2a) both suggest that the unpaired electron resides heavily on the terpyridine ligand and that the proper electronic description of this nickel complex is a Ni(II)-methyl cation bound to a reduced terpyridine ligand. Thus, an important consequence of these results is that alkyl halide reduction by (terpyridine)NiR(alkyl) complexes appears to be substantially ligand based. A comprehensive survey investigating the catalytic reactivity of related ligand derivatives suggests that electronic factors only moderately influence reactivity in the terpyridine-based catalysis and that the most dramatic effects arise from steric and solubility factors.
Optimizing Li+ conductivity in a garnet framework (2012)

The garnet-related oxides with the general formula Li7−xLa3Zr2−xTaxO12 (0 ≤ x ≤ 1) were prepared by conventional solid-state reaction. X-ray diffraction (XRD), neutron diffraction and AC impedance were used to determine phase formation and the lithium-ion conductivity. The lattice parameter of Li7−xLa3Zr2−xTaxO12 decreased linearly with increasing x. Optimum Li-ion conductivity in the Li-ion garnets Li7−xLa3Zr2−xTaxO12 is found in the range 0.4 ≤ x ≤ 0.6 for samples fired at 1140 °C in an alumina crucible. A room-temperature σLi ≈ 1.0 × 10−3 S cm−1 for x = 0.6 with an activation energy of 0.35 eV in the temperature range of 298–430 K makes this Li-ion solid electrolyte attractive for a new family of Li-ion rechargeable batteries.
Role of Acid pH and Deficient Efflux of Pyrazinoic Acid in Unique Susceptibility of <i>Mycobacterium tuberculosis</i> to Pyrazinamide (1999)

Pyrazinamide (PZA) is an important antituberculosis drug. Unlike most antibacterial agents, PZA, despite its remarkable in vivo activity, has no activity against Mycobacterium tuberculosis in vitro except at an acidic pH. M. tuberculosis is uniquely susceptible to PZA, but other mycobacteria as well as nonmycobacteria are intrinsically resistant. The role of acidic pH in PZA action and the basis for the unique PZA susceptibility of M. tuberculosis are unknown. We found that in M. tuberculosis, acidic pH enhanced the intracellular accumulation of pyrazinoic acid (POA), the active derivative of PZA, after conversion of PZA by pyrazinamidase. In contrast, at neutral or alkaline pH, POA was mainly found outside M. tuberculosis cells. PZA-resistant M. tuberculosis complex organisms did not convert PZA into POA. Unlike M. tuberculosis, intrinsically PZA-resistant M. smegmatis converted PZA into POA, but it did not accumulate POA even at an acidic pH, due to a very active POA efflux mechanism. We propose that a deficient POA efflux mechanism underlies the unique susceptibility of M. tuberculosis to PZA and that the natural PZA resistance of M. smegmatis is due to a highly active efflux pump. These findings may have implications with regard to the design of new antimycobacterial drugs.