gebhart/patrepeval huggingface dataset:
Early events of vesicular–arbuscular mycorrhiza formation on Ri T‐DNA transformed roots (1988)

An in vitro system using Ri T-DXA transformed roots and the vesicular-arbuscular mycorrhizal fungus Gigaspora margarita Becker & Hall has been developed to study the initial events of mycorrhiza formation. Sucrose, sodium and phosphorus were found to be critical components of the medium used to establish the dual culture. Using a single spore as inoculum it was consistently possible to obtain colonization of a preselected point on the root and to time the colonization process (within 5 days). Abundant viable and aseptic spores can be obtained. The system is especially appropriate for studying the triggering of the fungal biotrophy towards the root.
Metabotropic suppression of excitation in murine autaptic hippocampal neurons (2006)

Depolarization-induced suppression of excitation (DSE) and inhibition (DSI) are forms of short-term neuronal plasticity involving postsynaptic release of an endocannabinoid and the activation of presynaptic cannabinoid CB1 receptors. We have recently reported that CB1-dependent DSE can be elicited in autaptic cultures of excitatory hippocampal neurons of the mouse. We now report that the same preparation exhibits a parallel G(q)-coupled receptor-dependent production of endocannabinoids causing retrograde inhibition, also via CB1 receptors, which we will refer to as metabotropic suppression of excitation (MSE). We tested a spectrum of G(q)-coupled receptor agonists and found that both muscarinic and metabotropic glutamate receptors (group I) mediate retrograde inhibition via CB1 receptors in autaptic hippocampal neurons. Thus these neurons possess not only the pre- and postsynaptic machinery necessary for DSE but also that for MSE. This permitted a closer examination of MSE and its interaction with other aspects of the endocannabinoid retrograde signalling machinery: MSE mimics and occludes DSE and is itself occluded by the endocannabinoid 2-arachidonoyl glycerol (2-AG), consistent with 2-AG as a likely mediator of MSE. In contrast to DSE, MSE undergoes heterologous desensitization over the time course of minutes. In keeping with data reported for metabotropic suppression of inhibition (MSI) and DSI in the hippocampus, subthreshold MSE and DSE act synergistically. We additionally found that Delta9-tetrahydrocannabinol, which has been shown to attenuate DSE, antagonizes MSE. Finally, we have distinguished a neuronal subpopulation that exhibits DSE and a differential complement of MSE-mediating Gq-coupled receptors, making possible contrasting studies of MSE. Autaptic endocannabinoid signalling is rich, robust and complex in a deceptively simple package, including a previously unreported postsynaptic mechanism of adaptation in addition to known presynaptic CB1 desensitization. These adaptive sites offer novel targets for modulation of endogenous cannabinoid signalling.
Endogenous metabolism by sperm in response to altered cellular ATP requirements (1985)

A quantitative description of the relative importance of endogenous metabolism to overall ATP production has not been established for mammalian cells. We report herein results of experiments using sperm (selected because of their simple metabolic potential and absence of biosynthetic pathways) and calorimetry (chosen because it serves as a general monitor of metabolism) to assess the importance of endogenous metabolism to total ATP synthesis under several incubation conditions. In experiments in which sperm were incubated at different temperatures (20 degrees C, 25 degrees C, 30 degrees C or 35 degrees C) and with different substrates (glucose, fructose, lactate, or beta-hydroxybutyrate), endogenous metabolism occurred at a constant rate regardless of the rate of ATP turnover in the cells or the nature of the exogenous substrate available to them. Sperm incubated at 35 degrees C with glycolyzable substrates synthesized more ATP (9 mumol ATP . h-1/10(8) cells) than did sperm incubated with the nonglycolyzable substrate, lactate (6.2 mumol ATP . h-1/10(8) cells). To investigate this substrate-related difference in the rate of ATP synthesis, the motility of sperm incubated at 35 degrees C with glucose or with lactate was determined. The velocities of the sperm incubated with either substrate were identical, indicating that the rates of ATP consumption for support of motility were identical. Most of the additional ATP synthesized by cells with glycolyzable substrates was consumed in the process of substrate cycling of the metabolic intermediates of glucose.
Mining the antibodyome for HIV-1–neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains (2013)

Next-generation sequencing of antibody transcripts from HIV-1-infected individuals with broadly neutralizing antibodies could provide an efficient means for identifying somatic variants and characterizing their lineages. Here, we used 454 pyrosequencing and identity/divergence grid sampling to analyze heavy- and light-chain sequences from donor N152, the source of the broadly neutralizing antibody 10E8. We identified variants with up to 28% difference in amino acid sequence. Heavy- and light-chain phylogenetic trees of identified 10E8 variants displayed similar architectures, and 10E8 variants reconstituted from matched and unmatched phylogenetic branches displayed significantly lower autoreactivity when matched. To test the generality of phylogenetic pairing, we analyzed donor International AIDS Vaccine Initiative 84, the source of antibodies PGT141-145. Heavy- and light-chain phylogenetic trees of PGT141-145 somatic variants also displayed remarkably similar architectures; in this case, branch pairings could be anchored by known PGT141-145 antibodies. Altogether, our findings suggest that phylogenetic matching of heavy and light chains can provide a means to approximate natural pairings.
RamA Is an Alternate Activator of the Multidrug Resistance Cascade in Enterobacter aerogenes (2004)

Multidrug resistance (MDR) in Enterobacter aerogenes can be mediated by induction of MarA, which is triggered by certain antibiotics and phenolic compounds. In this study, we identified the gene encoding RamA, a 113-amino-acid regulatory protein belonging to the AraC-XylS transcriptional activator family, in the Enterobacter aerogenes ATCC 13048 type strain and in a clinical multiresistant isolate. Overexpression of RamA induced an MDR phenotype in drug-susceptible Escherichia coli JM109 and E. aerogenes ATCC 13048, as demonstrated by 2- to 16-fold-increased resistance to beta-lactams, tetracycline, chloramphenicol, and quinolones, a decrease in porin production, and increased production of AcrA, a component of the AcrAB-TolC drug efflux pump. We show that RamA enhances the transcription of the marRAB operon but is also able to induce an MDR phenotype in a mar-deleted strain. We demonstrate here that RamA is a transcriptional activator of the Mar regulon and is also a self-governing activator of the MDR cascade.
Recombinant Activated Factor VII for Adjunctive Hemorrhage Control in Trauma (2001)

The results of this report suggest that in trauma patients rFVIIa may play a role as an adjunctive hemostatic measure, in addition to surgical hemostatic techniques, and provides the motivation for controlled animal and clinical trials.
Differences in glycosylation patterns of closely related murine leukemia viruses (1980)

The nature of the carbohydrate chains in the major envelope glycoprotein of murine leukemia virus, gp70, and its cellular precursor has been investigated. A difference in the oligosaccharide composition of gp70 from an ecotropic murine leukemia virus (Akv) and three recombinant dual-tropic viruses [mink cell focus-inducing viruses (MCFs)] derived from Akv was demonstrated. Glycosidase digestion and gel filtration were utilized to identify the two classes of N-asparagine-linked oligosaccharides, high-mannose and complex. The gp70 of the ecotropic virus contained only N-linked oligosaccharides of the complex type. In contrast, the gp70s of the dual-tropic viruses contained both high-mannose and complex oligosaccharides. Analysis of gp70 glycopeptides from an MCF-related xenotropic virus showed an elution profile similar, but not identical, to profiles of the MCFs. The gp70 precursors isolated from cells infected with Akv or MCF virus contained N-linked oligosaccharides that were exclusively of the high-mannose type. Comparison of the high-mannose oligosaccharides of the MCF gp70 precursors with those of the corresponding gp70s indicated that very little further processing of the high-mannose residues in the gp70s had occurred. The presence of the high-mannose oligosaccharides in the envelope glycoprotein of the dual-tropic viruses results from altered carbohydrate processing. The conservation of this altered carbohydrate pattern in a number of hosts and under various conditions of growth suggests that the viral protein structure is the primary factor in determining the different mode of glycosylation of the MCF gp70s. Thus, these viral glycoproteins provide an important model system for studying the relationship between protein structure and patterns of glycosylation.
Epidemic algorithms for replicated database maintenance (1987)

Whru a dilt~lhSC is replicated at, many sites2 maintaining mutual consistrnry among t,he sites iu the fac:e of updat,es is a signitirant problem. This paper descrikrs several randomized algorit,hms for dist,rihut.ing updates and driving t,he replicas toward consist,c>nc,y. The algorit Inns are very simple and require few guarant,ees from the underlying conllllunicat.ioll system, yc+ they rnsutc t.hat. the off(~c~t, of ('very update is evcnt,uwlly rf+irt-ted in a11 rq1ica.s. The cost, and parformancc of t,hr algorithms arc tuned I>? c%oosing appropriat,c dist,rilMions in t,hc randoinizat,ioii step. TIN> idgoritlmls ilr(' c*los~*ly analogoIls t,o epidemics, and t,he epi-dcWliolog)-litc\ratiirc, ilitlh iii Illld~~rsti4lldill~ tlicir bc*liavior. One of tlW i$,oritlims 11&S brc>n implrmcWrd in the Clraringhousr sprv(brs of thr Xerox C'orporat~c~ Iiitcrnc4, solviiig long-standing prol>lf~lns of high traffic and tlatirl>ilsr inconsistcllcp.
Botrytis cinerea virulence is drastically reduced after disruption of chitin synthase class III gene (Bcchs3a) (2006)

Botrytis cinerea is an important phytopathogenic fungus requiring new methods of control. Chitin biosynthesis, which involves seven classes of chitin synthases, could be an attractive target. A fragment encoding one of the class III enzymes was used to disrupt the corresponding Bcchs3a gene in the B. cinerea genome. The resulting mutant exhibited a 39% reduction in its chitin content and an 89% reduction in its in vitro chitin synthase activity, compared with the wild-type strain. Bcchs3a mutant was not affected in its growth in liquid medium, neither in its production of sclerotia, micro- and macroconidia. In contrast, the mutant Bcchs3a was severely impaired in its growth on solid medium. Counterbalancing this defect in radial growth, Bcchs3a mutant presented a large increase in hyphal ramification, resulting in an enhanced aerial growth. Observations by different techniques of microscopy revealed a thick extracellular matrix around the hyphal tips. Moreover, Bcchs3a mutant had a largely reduced virulence on Vitis vinifera and Arabidopsis thaliana leaves.
Antibacterial Activities of Poly(amidoamine) Dendrimers Terminated with Amino and Poly(ethylene glycol) Groups (2007)

Poly(amidoamine) (PAMAM) dendrimer derivatives have been investigated for their biological applications, especially for delivery of drugs, including antimicrobial drugs to eukaryotic cells, but their effects on bacterial cells are largely unexplored. Herein we report that amino-terminated PAMAM dendrimers are highly toxic to the common Gram-negative pathogen Pseudomonas aeruginosa. The concentration that kills 50% of the bacteria (EC50) was in the range of approximately 0.9-1.5 microg/mL for the generation 5, amino-terminated dendrimers with or without partial (43%) coating of poly(ethylene glycol) (PEG). These EC50 values were lower than that ( approximately 1.9-2.8 microg/mL) for LL-37, a potent antimicrobial peptide expressed in a variety of epithelia. On the contrary, the dendrimers were far less toxic (EC50 > 21 microg/mL) to the Gram-positive pathogen Staphylococcus aureus than LL-37 (EC50 = approximately 1.9 microg/mL). In agreement with the previous studies on other cell types, the dendrimers were not cytotoxic to human corneal epithelial cells at the concentrations that were toxic to P. aeruginosa. Our findings indicate that amino-terminated PAMAM dendrimers and their partially PEG-coated derivatives possess attractive antimicrobial properties, particularly against Gram-negative bacteria, thus expanding the potential biological application of the dendrimers.
Mediators of tubuloglomerular feedback regulation of glomerular filtration: ATP and adenosine (2006)

In the juxtaglomerular apparatus of the kidney the loop of Henle gets into close contact to its parent glomerulus. This anatomical link between the tubular system and the vasculature of the afferent and efferent arteriole enables specialized tubular cells, the macula densa (MD) cells, to establish an intra-nephron feedback loop designed to control preglomerular resistance and thereby single nephron glomerular filtration rate. This review focuses on the signalling mechanisms which link salt-sensing MD cells and the regulation of preglomerular resistance, a feedback loop known as tubuloglomerular feedback (TGF). Two purinergic molecules, ATP and adenosine, have emerged over the years as most likely candidates to serve as mediators of TGF. Data will be reviewed supporting a role of either ATP or adenosine as mediators of TGF. In addition, a concept will be discussed that integrates both ATP and adenosine into one signalling cascade that includes (i) release of ATP from MD cells upon increases in tubular salt concentration, (ii) extracellular degradation of ATP to form adenosine, and (iii) adenosine-mediated vasoconstriction of the afferent arteriole.
Oxaloacetate Hydrolase, the C–C Bond Lyase of Oxalate Secreting Fungi (2007)

Oxalate secretion by fungi is known to be associated with fungal pathogenesis. In addition, oxalate toxicity is a concern for the commercial application of fungi in the food and drug industries. Although oxalate is generated through several different biochemical pathways, oxaloacetate acetylhydrolase (OAH)-catalyzed hydrolytic cleavage of oxaloacetate appears to be an especially important route. Below, we report the cloning of the Botrytis cinerea oahA gene and the demonstration that the disruption of this gene results in the loss of oxalate formation. In addition, through complementation we have shown that the intact B. cinerea oahA gene restores oxalate production in an Aspergillus niger mutant strain, lacking a functional oahA gene. These observations clearly indicate that oxalate production in A. niger and B. cinerea is solely dependent on the hydrolytic cleavage of oxaloacetate catalyzed by OAH. In addition, the B. cinera oahA gene was overexpressed in Escherichia coli and the purified OAH was used to define catalytic efficiency, substrate specificity, and metal ion activation. These results are reported along with the discovery of the mechanism-based, tight binding OAH inhibitor 3,3-difluorooxaloacetate (K(i) = 68 nM). Finally, we propose that cellular uptake of this inhibitor could reduce oxalate production.
Story Albums: Creating Fictional Stories From Personal Photograph Sets (2017)

Abstract We present a method for the automatic creation of fictional storybooks based on personal photographs. Unlike previous attempts that summarize such collections by picking salient or diverse photos, or creating personal literal narratives, we focus on the creation of fictional stories. This provides new value to users, as well as an engaging way for people (especially children) to experience their own photographs. We use a graph model to represent an artist‐generated story, where each node is a ‘frame’, akin to frames in comics or storyboards. A node is described by story elements, comprising actors, location, supporting objects and time. The edges in the graph encode connections between these elements and provide the discourse of the story. Based on this construction, we develop a constraint satisfaction algorithm for one‐to‐one assignment of nodes to photographs. Once each node is assigned to a photograph, a visual depiction of the story can be generated in different styles using various templates. We show results of several fictional visual stories created from different personal photo sets and in different styles.
CHEMICAL CONTROL OF GENE EXPRESSION (1997)

Promoters that respond to otherwise inactive chemicals will enhance the tools available for analyzing gene function in vivo and for altering defined traits of plants at will. Approaches to provide such tools have yielded plant promoters that respond to compounds activating defense genes. In addition, the transfer of regulatory elements from prokaryotes, insects, and mammals has opened new avenues to construct chemically inducible promoters that respond to signals normally not recognized by plants. This review describes results and applications of these two approaches.
Metabolic control during preimplantation mammalian development (1995)

Metabolic control during preimplantation development may be either intrinsic to the embryo or extrinsic, i.e. mediated via the environment within the female tract. Intrinsic control is exhibited by early preimplantation embryos, which are undifferentiated, largely autonomous and show no growth. The best characterized intrinsic metabolic control mechanism is the switch from pyruvate to glucose as major energy substrate during mouse preimplantation development. A shift to extrinsic control occurs during the later preimplantation stages, when differentiation into trophectoderm and inner cell mass occurs, net growth begins and the embryo prepares for implantation. Thus, the environment provided by the oviduct, in which the embryos of most mammalian species spend their first 3 days, may be considered as facilitatory rather than obligatory for early embryo development, whereas the uterine environment is required to provide a more complex milieu. The 'facilitators' provided by the oviduct include physical factors, such as ciliary and muscular action, and chemical factors, including oxygen, nutrients, ions and macromolecules. Oviduct fluid secretion is under adrenergic influence, defects in which could contribute to impaired mucosal defence and tubal blockage in women. Preimplantation embryos exhibit metabolic adaptation, whereby their metabolism responds to changes in the external environment. Such adaptation explains the ability of early embryos to develop in a variety of culture media, a situation similar to that which they will experience in the female tract. Thus, the provision of a variety of media in vitro is likely to ensure the development of embryos in a physiological manner.
Exchanging Interleukin-8 and Melanoma Growth-stimulating Activity Receptor Binding Specificities (1996)

Interleukin-8 (IL-8), a CXC chemokine, is known to bring about chemotaxis and activation of neutrophils through high affinity binding to at least two distinct receptors, receptor-A and receptor-B. The IL-8 homolog melanoma growth stimulating activity (MGSA) is also active toward neutrophils. In contrast to IL-8, MGSA binds receptor-B with high affinity and binds receptor-A with approximately 400-fold lower affinity. Using the structure of IL-8 (Clore et al.(1990) Biochemistry, 29, 1689-1696; Baldwin et al. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 502-506) and the NMR-determined structure of MGSA (Fairbrother et al. (1994) J. Mol. Biol. 242, 252-270), we designed variants of both IL-8 and MGSA to investigate the basis of specificity for binding of these chemokines to the IL-8 receptors. The most outstanding structural difference between IL-8 and MGSA lies in the loop preceding the first beta-strand. When the corresponding (shorter) loop from MGSA was swapped into IL-8, both receptor-A and receptor-B binding affinities were significantly (>300-fold) reduced. However, with additional mutations that affect packing interactions, an IL-8 variant specific for receptor-B binding was produced. Conversely, when the same loop from IL-8 was swapped into MGSA, receptor-B binding was maintained with only a approximately 30-fold reduction in receptor-A affinity. Again, mutations affecting packing of the loop yielded a MGSA variant with high affinity for both receptors, like IL-8. Finally, we show, through point mutations in a monomeric IL-8 framework, that individual side chain substitutions can affect receptor specificity.
Heterogeneous photocatalytic oxidation of cyanide and sulfite in aqueous solutions at semiconductor powders (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHeterogeneous photocatalytic oxidation of cyanide and sulfite in aqueous solutions at semiconductor powdersSteven N. Frank and Allen J. BardCite this: J. Phys. Chem. 1977, 81, 15, 1484–1488Publication Date (Print):July 1, 1977Publication History Published online1 May 2002Published inissue 1 July 1977https://pubs.acs.org/doi/10.1021/j100530a011https://doi.org/10.1021/j100530a011research-articleACS PublicationsRequest reuse permissionsArticle Views2414Altmetric-Citations496LEARN 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 options Get e-Alerts
Defence Solicitors in Criminal Cases: An Introduction (1994)

Abstract This chapter concentrates on solicitors and their staff and the nature and quality of the legal defence and ‘representation’ they provide to these clients on a routine basis. It starts by presenting the development of criminal defence. While recommending that legal aid for trials in the higher criminal courts and for committals should be the norm, the Widgery Committee argued that legal representation for magistrates' court defendants should remain a minority phenomenon and that legal aid should be granted only in certain specified circumstances, under what were to become known as the ‘Widgery criteria’. The data cannot be claimed that the forty-eight firms of solicitors constitute a fully representative sample of the total of between 6,000 and 7,000 separate solicitors' offices in the country who undertake criminal defence work under legal aid each year.