gebhart/patrepeval huggingface dataset:
Microarray analysis of chitin elicitation in Arabidopsis thaliana (2002)

Summary Chitin oligomers, released from fungal cell walls by endochitinase, induce defence and related cellular responses in many plants. However, little is known about chitin responses in the model plant Arabidopsis. We describe here a large-scale characterization of gene expression patterns in Arabidopsis in response to chitin treatment using an Arabidopsis microarray consisting of 2375 EST clones representing putative defence-related and regulatory genes. Transcript levels for 71 ESTs, representing 61 genes, were altered three-fold or more in chitin-treated seedlings relative to control seedlings. A number of transcripts exhibited altered accumulation as early as 10 min after exposure to chitin, representing some of the earliest changes in gene expression observed in chitin-treated plants. Included among the 61 genes were those that have been reported to be elicited by various pathogen-related stimuli in other plants. Additional genes, including genes of unknown function, were also identified, broadening our understanding of chitin-elicited responses. Among transcripts with enhanced accumulation, one cluster was enriched in genes with both the W-box promoter element and a novel regulatory element. In addition, a number of transcripts had decreased abundance, encoding several proteins involved in cell wall strengthening and wall deposition. The chalcone synthase promoter element was identified in the upstream regions of these genes, suggesting that pathogen signals may suppress the expression of some genes. These data indicate that Arabidopsis should be an excellent model to elucidate the mechanisms of chitin elicitation in plant defence.
Determinants for selective RAR and TR recognition of direct repeat HREs. (1993)

Recently, we have shown that receptors for vitamin D3 (VDR), thyroid hormone (TR), and retinoic acid (RAR) activate preferentially through direct repeats (DRs) spaced by 3, 4, and 5 nucleotides, respectively. In addition, the RAR can activate weakly through DRs spaced by 2 nucleotides. A common feature of RAR, TR, and VDR is their ability to heterodimerize with the retinoid X receptor (RXR) through their ligand-binding domains (LBDs) to form high-affinity DNA-binding complexes that are specific for appropriately spaced repeats. In this paper we demonstrate that selective binding of RAR-RXR and TR-RXR heterodimers to their cognate DRs is a consequence of a novel cooperative dimer interaction within the DNA-binding domains (DBDs). Accordingly, a region in the first zinc finger of the TR and RAR DBDs interacts with the second zinc finger in the RXR DBD to promote selective DNA-binding to DRs spaced by 4 and 5 nucleotides, respectively. The resulting polarity established by this interaction places RXR in the 5' position of the direct repeats. These data provide a mechanism for selective receptor recognition of a restricted set of target sequences in DR DNA and explains the structural basis for physiological specificity.
The Analgesic Efficacy of Subarachnoid Morphine in Comparison with Ultrasound-Guided Transversus Abdominis Plane Block After Cesarean Delivery (2010)

As part of a multimodal analgesic regimen, subarachnoid morphine provided superior analgesia when compared with ultrasound-guided transversus abdominis plane block after cesarean delivery, yet at the cost of increased side effects.
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction (2002)

In this paper, we introduce a method to account for the shape of the potential energy curve in the evaluation of conformational free energies. The method is based on a procedure that generates a set of conformations, each with its own force-field energy, but adds a term to this energy that favors conformations that are close in structure (have a low rmsd) to other conformations. The sum of the force-field energy and rmsd-dependent term is defined here as the "colony energy" of a given conformation, because each conformation that is generated is viewed as representing a colony of points. The use of the colony energy tends to select conformations that are located in broad energy basins. The approach is applied to the ab initio prediction of the conformations of all of the loops in a dataset of 135 nonredundant proteins. By using an rmsd from a native criterion based on the superposition of loop stems, the average rmsd of 5-, 6-, 7-, and 8-residue long loops is 0.85, 0.92, 1.23, and 1.45 A, respectively. For 8-residue loops, 60 of 61 predictions have an rmsd of less than 3.0 A. The use of the colony energy is found to improve significantly the results obtained from the potential function alone. (The loop prediction program, "Loopy," can be downloaded at http://trantor.bioc.columbia.edu.)
Down-regulation of OATP1B proteins correlates with hyperbilirubinemia in advanced cholestasis. (2015)

Down-regulation of OATP1B proteins may contribute to pathogenesis of jaundice accompanying advanced cholestatic liver diseases.
CHARACTERIZATION OF INTESTINAL γδ T-CELLS IN COELIAC DISEASE (1991)

Depts. of Immunohaematology, Gastroenterology, Pediatrics and Pathology, Academic Hospital, Leiden, The Netherlands.
Reliable Method for Driving Events Recognition (2005)

Motor vehicles greatly influence human life but are also a major cause of death and road congestion, which is an obstacle to future economic development. We believe that by learning driving patterns, useful navigation support can be provided for drivers. In this paper, we present a simple and reliable method for the recognition of driving events using hidden Markov models (HMMs), popular stochastic tools for studying time series data. A data acquisition system was used to collect longitudinal and lateral acceleration and speed data from a real vehicle in a normal driving environment. Data were filtered, normalized, segmented, and quantified to obtain the symbolic representation necessary for use with discrete HMMs. Observation sequences for training and evaluation were manually selected and classified as events of a particular type. An appropriate model size was selected, and the model was trained for each type of driving events. Observation sequences from the training set were evaluated by multiple models, and the highest probability decides what kind of driving event this sequence represents. The recognition results showed that HMMs could recognize driving events very accurately and reliably.
C1q enhances the phagocytosis of Cryptococcus neoformans blastospores by human monocytes. (1988)

We investigated whether C1q, a subunit of the first component of C, could modulate human peripheral blood monocyte-mediated phagocytosis of Cryptococcus neoformans (CN). Adherence of monocytes to C1q-coated surfaces induced a significant enhancement of ingestion of CN blastospores that had been opsonized with specific anticapsular IgG (IgG-CN). Additionally, C1q enhanced the monocyte-mediated phagocytosis of CN opsonized with C (CN-absorbed, nonimmune, normal human serum; C-CN). Ingestion of IgG- and C-CN by control and C1q-stimulated monocytes was maximal by 1 h of incubation. The monocyte-mediated enhancement of phagocytosis caused by C1q was paralleled by a proportionate increase in fungicidal activity, an effect which was maximal by 3 h of incubation. Human serum albumin-adherent, control monocytes exhibited only a low level of killing after 3 h of incubation. C1q enhancement was blocked by preincubation of the surfaces with a goat, polyclonal F(ab')2 anti-C1q. This study describes a new cellular function for the cell surface C1q receptor: the enhancement of phagocytosis of a pathogenic organism by monocytes.
Automated Process for Improved Uniformity and Versatility of Layer-by-Layer Deposition (2007)

The recently developed practice of spraying polyelectrolyte solutions onto a substrate in order to construct thin films via the layer-by-layer technique has been further investigated and extended. Here we describe a fully automated system capable of depositing thin polymer films from atomized mists of solutions containing species of complementary functionality. Film growth is shown to be similar to that in conventional "dipped" LbL assembly, whereas the reported technology allows us to realize 25-fold decreases in process times. Furthermore, complete automation removes human interaction and the possibility of operator-induced nonuniformities. We extend the versatility of the spray LbL technology by depositing both weak and strong polyelectrolyte films, hydrogen-bonded films, and dendritic compounds and nanoparticles, broadening its range of future applications. Finally, the technology is used to uniformly coat an otherwise hydrophobic substrate from aqueous solutions. ESEM images indicate that the atomization process produces a conformal coating of individual nanofibers within the substrate, dramatically changing the hydrophilicity of the macroscopic surface. Such an automated system is easily converted to an array of nozzle banks and could find application in the rapid, uniform coating of large areas of textile materials.
Impact of early parenteral nutrition completing enteral nutrition in adult critically ill patients (EPaNIC trial): a study protocol and statistical analysis plan for a randomized controlled trial (2011)

ClinicalTrials (NCT): NCT00512122.
Evidence for Ligand-Dependent Intramolecular Folding of the AF-2 Domain in Vitamin D Receptor-Activated Transcription and Coactivator Interaction (1997)

A ligand-dependent transcriptional activation domain (AF-2) exists in region E of the nuclear receptors. This highly conserved domain may contact several coactivators that are putatively involved in nuclear receptor-mediated transcription. In this study, a panel of vitamin D receptor (VDR) AF-2 mutants was created to examine the importance of several conserved residues in VDR-activated transcription. Two AF-2 mutants (L417S and E420Q) exhibited normal ligand binding, heterodimerization with retinoid X receptor, and vitamin D-responsive element interaction, but they were transcriptionally inactive in a VDR-responsive reporter gene assay. All AF-2 mutations that abolished VDR-mediated transactivation also eliminated interactions between VDR and several putative coactivator proteins including suppressor of gal1 (SUG1), steroid hormone receptor coactivator-1 (SRC-1), or receptor interacting protein (RIP140), suggesting that coactivator interaction is important for AF-2-mediated transcription. In support of this concept, the minimal AF-2 domain [VDR(408-427)] fused to the gal4 DNA binding domain was sufficient to mediate transactivation as well as interaction with putative coactivators. Introducing the L417S and E420Q mutations into the minimal AF-2 domain abolished this autonomous transactivation and coactivator interactions. Finally, we demonstrate that the minimal AF-2 domain interacted with an AF-2 deletion mutant of the VDR in a 1,25-(OH)2D3-dependent manner, suggesting a ligand-induced intramolecular folding of the VDR AF-2 domain. The L417S mutant of this domain disrupted the interaction with VDR ligand-binding domain, while the E420Q mutant did not affect this interaction. These studies suggest that the conserved AF-2 motif may mediate transactivation through ligand-dependent intermolecular interaction with coactivators and through ligand-induced intramolecular contacts with the VDR ligand-binding domain itself.
Operational stability of electrophosphorescent devices containing p and n doped transport layers (2003)

The operational stability of low-operating voltage p-i-n electrophosphorescent devices containing fac-tris(2-phenylpyridine) iridium as the emissive dopant is investigated. In these devices, Li-doped 4,7-diphenyl-1,10-phenanthroline (BPhen) served as an n-type electron transport layer, or as an undoped hole blocking layer (HBL), and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane doped 4,4′,4″-tris(3-methylphenylphenylamino) triphenylamine served as a p-type hole transport layer. The glass transition temperature of BPhen can be increased by the addition of aluminum(III)bis(2-methyl-8-quinolinato)4-phenylphenolate (BAlq), resulting in improved morphological stability, thereby reducing device degradation. When thermally stable BAlq was used as a HBL in both p-i-n and undoped devices, the extrapolated operational lifetime (normalized to an initial luminance of 100 cd/m2) of the p-i-n and undoped devices are 18 000 and 60 000 h, respectively, indicating that the presence of p and n dopants can accelerate device degradation.
Regulation of antibacterial defense in the small intestine by the nuclear bile acid receptor (2006)

Obstruction of bile flow results in bacterial proliferation and mucosal injury in the small intestine that can lead to the translocation of bacteria across the epithelial barrier and systemic infection. These adverse effects of biliary obstruction can be inhibited by administration of bile acids. Here we show that the farnesoid X receptor (FXR), a nuclear receptor for bile acids, induces genes involved in enteroprotection and inhibits bacterial overgrowth and mucosal injury in ileum caused by bile duct ligation. Mice lacking FXR have increased ileal levels of bacteria and a compromised epithelial barrier. These findings reveal a central role for FXR in protecting the distal small intestine from bacterial invasion and suggest that FXR agonists may prevent epithelial deterioration and bacterial translocation in patients with impaired bile flow.
To the Rescue: Curtis Ann (Montana) (2015)

IN BIG WATER.Sheo lived much of her life in a 70-gallon tank about the size of a bathtub.By most standards, her setup was spacious.But once she was let loose in a 2,000-gallon tank, her spirit soared.A photo of her in the tank shows her floating, legs stretched out."She couldn't do that ... at home:' says Wendy Graff, her former owner."I could tell she was so happy:'Curtis Ann was one of dozens of red-eared slider turtles turned in after Montana banned the species last summer.The nonnative turtles, most likely released pets and their offspring, are turning up in local waterways, where they outcompete natives such as painted turtles for food and habitat.With no more selling of red-eared sliders in the state and the requirement for existing pet owners to purchase an exotic species license, the turn-in seemed like the per fect solution.Working with HSU S wildlife specialist Dave Pauli, the Montana Fish, Wildlife and Parks department created a program to take in pet turtles with the goal of rehabilitating them for release in their native range, a block of states in the south-central U.S. 6 allanimals // MAY/JUNE 2015 HSU5-wlldllfe specialist Dave Paull checks on the former pet turtles as they ll4apt tq more spadous living quarters.
Transposon Tn10 contains two structural genes with opposite polarity between tetA and IS10R (1984)

The nucleotide sequence of the central part of Tn10 has been determined from the rightmost HindIII site to IS10R. This sequence contains two open reading frames with opposite polarity. The in vivo transcription start points in this sequence have been determined by S1 mapping. These results define one minor and two major promoters. The transcription starts of the two major promoters are only 18 base pairs apart, and the transcripts show different polarity and overlap by 18 base pairs. The nucleotide sequence reveals two regions with palindromic symmetry which may serve as operators. Their possible involvement in the regulation of transcription of both genes is discussed. Taken together these results allow for a maximal coding capacity of 138 amino acids directed toward IS10R and 197 amino acids directed toward tetA. The possible function of these gene products is discussed. The accompanying article (Braus et al., J. Bacteriol. 160:504-509, 1984) presents evidence that these genes are expressed.
Multifunctional Prenylated Peptides for Live Cell Analysis (2009)

Protein prenylation is a common post-translational modification present in eukaryotic cells. Many key proteins involved in signal transduction pathways are prenylated, and inhibition of prenylation can be useful as a therapeutic intervention. While significant progress has been made in understanding protein prenylation in vitro, we have been interested in studying this process in living cells, including the question of where prenylated molecules localize. Here, we describe the synthesis and live cell analysis of a series of fluorescently labeled multifunctional peptides, based on the C-terminus of the naturally prenylated protein CDC42. A synthetic route was developed that features a key Acm to Scm protecting group conversion. This strategy was compatible with acid-sensitive isoprenoid moieties and allowed incorporation of an appropriate fluorophore as well as a cell-penetrating sequence (penetratin). These peptides are able to enter cells through different mechanisms, depending on the presence or absence of the penetratin vehicle and the nature of the prenyl group attached. Interestingly, prenylated peptides lacking penetratin are able to enter cells freely through an energy-independent process and localize in a perinuclear fashion. This effect extends to a prenylated peptide that includes a full "CAAX box" sequence (specifically, CVLL). Hence, these peptides open the door for studies of protein prenylation in living cells, including enzymatic processing and intracellular peptide trafficking. Moreover, the synthetic strategy developed here should be useful for the assembly of other types of peptides that contain acid-sensitive functionalities.
A 19nm 112.8mm<sup>2</sup> 64Gb multi-level flash memory with 400Mb/s/pin 1.8V Toggle Mode interface (2012)

NAND flash memory is widely used in digital cameras, USB devices, cell phones, camcorders and solid-state drives. Continuous lowering of bit cost, increasing flash-memory-die densities and improving performance have helped to expand flash markets. Recently, there are two different directions to meet market demands. One is lowering bit cost and increase memory density to the utmost limit, which is achieved by 4b/cell [1] or 3b/cell [2]. The other is focusing on high performance and high reliability. To meet both demands, we develop a 19nm 112.8mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> 64Gb 2b/cell NAND flash memory with the smallest die size ever reported. 15MB/s programming throughput and 400Mb/s/pin 1.8V Toggle Mode interface [3] are achieved for the first time. Die Micrograph and features are shown in Figure 25.1.1.
Interlayer Forces and Ultralow Sliding Friction in Multiwalled Carbon Nanotubes (2006)

We describe interlayer force measurements during prolonged, cyclic telescoping motion of a multiwalled carbon nanotube. The force acting between the core and the outer casing is modulated by the presence of stable defects and generally exhibits ultralow friction, below the measurement limit of 1.4 x 10(-15) N/atom and total dissipation per cycle lower than 0.4 meV/atom. Defects intentionally introduced in the form of dangling bonds lead to temporary mechanical dissipation, but the innate ability of nanotubes to self heal rapidly optimizes the atomic structure and restores smooth motion.
Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. III. A polymerase-primase interaction governs primer size. (1992)

Studies with a rolling-circle DNA replication system reconstituted in vitro with a tailed form II DNA template, the DNA polymerase III holoenzyme (Pol III HE), the Escherichia coli single-stranded DNA binding protein, and the primosome, showed that within the context of a replication fork, the oligoribonucleotide primers that were formed were limited to a length in the range of 9 to 14 nucleotides, regardless of whether they were subsequently elongated by the lagging-strand DNA polymerase. This is in contrast to the 8-60-nucleotide-long primers synthesized by the primosome in the absence of DNA replication on a bacteriophage phi X174 DNA template, although when primer synthesis and DNA replication were catalyzed concurrently in this system, the extent of RNA polymerization decreased. As described in this report, we therefore examined the effect of the DNA Pol III HE on the length of primers synthesized by primase in vitro in the absence of DNA replication. When primer synthesis was catalyzed either: i) by the primosome on a phi X174 DNA template, ii) by primase on naked DNA with the aid of the DnaB protein (general priming), or iii) by primase alone at the bacteriophage G4 origin, the presence of the DNA Pol III HE in the reaction mixtures resulted in a universal reduction in the length of the heterogeneous RNA products to a uniform size of approximately 10 nucleotides. dNTPs were not required, and the addition of dGMP, an inhibitor of the 3'----5' exonuclease of the DNA Pol III HE, did not alter the effect; therefore, neither the 5'----3' DNA polymerase activity nor the 3'----5' exonuclease activity of the DNA Pol III HE was involved. E. coli DNA polymerase I, and the DNA polymerases of bacteriophages T4 and T7 could not substitute for the DNA Pol III HE. The Pol III core plays a crucial role in mediating this effect, although other subunits of the DNA Pol III HE are also required. These observations suggest that the association of primase with the DNA Pol III HE during primer synthesis regulates its catalytic activity and that this regulatory interaction occurs independently of, and prior to, formation of a preinitiation complex of the DNA Pol III HE on the primer terminus.
Miscellaneous fused pyrimidines (1992)

Pyridopyrimidines. Pyrano- and Thiopyranopyrimidines. Pyrimidopyrimidines. Pyrimidopyridazines. Pyrimidooxazines and Pyrimidothiazines. Pyrimidotriazines. Index.
Macrophage cytoskeleton association with CR3 and CR4 regulates receptor mobility and phagocytosis of iC3b-opsonized erythrocytes (1992)

Abstract Alveolar macrophages (AMø) were examined for CR1 (C3b receptor, CD35), CR3 (iC3b receptor; CD11b/CD18), and CR4 (iC3b receptor; CD11c/CD18) by assays for binding of C3-opsonized sheep erythrocytes (EC3b or EC3bi) and uptake of specific monoclonal antibodies (mAbs). In AMø isolates from nine normal volunteers, 49% of cells bound EC3b and 71% bound EC3bi. Quantitation of receptors per cell with [125I]mAbs showed 8.5 × 104 CR4, 5.1 × 104 CR3, and 2.6 × 104 CR1. With most AMø preparations, CR3 was the major receptor mediating attachment of EC3bi, despite the predominance of CR4 antigens. Anti-CR3 inhibited EC3bi rosettes by ≥50%, whereas anti-CR4 blocked rosettes by ≤18%. U937 cells differentiated with phorbol myristate acetate resembled AMø in receptor expression but exhibited almost no CR4-dependent rosetting. Despite the relative inability of CR4 to mediate EC3bi attachment, AMø ingestion of [51Cr]EC3bi was blocked by either anti-CR3 or anti-CR4. Two lines of evidence indicated that CR3 were more mobile within the membrane than were CR4. Immunofluorescence staining demonstrated patching and occasional capping of CR3, whereas CR4 remained uniformly distributed. This patching and capping of CR3 required the actin cytoskeleton, as it was inhibited by cytochalasin D. Modulation experiments using surfaces coated with anti-CR3 or anti-CR4 also showed that CR3 was more mobile than was CR4. However, there was some variation among AMø isolates from different donors. In seven isolates, no CR4 modulation was produced with anti-CR4, whereas in six other isolates, CR4 was modulated by 66%. Incubation of cells in cytochalasin D increased modulation of both CR3 and CR4 on mAb-coated surfaces. Cells exhibiting increased mobility of CR4 showed an increased ability to form CR4-dependent EC3bi rosettes. The data are consistent with the hypothesis that CR3 and CR4 exhibit a variable association with the cytoskeleton that regulates their mobility and function. A relatively mobile subset of CR3 and/or CR4 mediates EC3bi attachment, whereas a relatively immobile subset of CR3 and/or CR4 fails to mediate EC3bi attachment but functions to promote ingestion of EC3bi.