gebhart/patrepeval huggingface dataset:
PMR6 , a Pectate Lyase–Like Gene Required for Powdery Mildew Susceptibility in Arabidopsis (2002)

The plant genes required for the growth and reproduction of plant pathogens are largely unknown. In an effort to identify these genes, we isolated Arabidopsis mutants that do not support the normal growth of the powdery mildew pathogen Erysiphe cichoracearum. Here, we report on the cloning and characterization of one of these genes, PMR6. PMR6 encodes a pectate lyase-like protein with a novel C-terminal domain. Consistent with its predicted gene function, mutations in PMR6 alter the composition of the plant cell wall, as shown by Fourier transform infrared spectroscopy. pmr6-mediated resistance requires neither salicylic acid nor the ability to perceive jasmonic acid or ethylene, indicating that the resistance mechanism does not require the activation of well-described defense pathways. Thus, pmr6 resistance represents a novel form of disease resistance based on the loss of a gene required during a compatible interaction rather than the activation of known host defense pathways.
Spatial splits in bounding volume hierarchies (2009)

Bounding volume hierarchies (BVH) have become a widely used alternative to kD-trees as the acceleration structure of choice in modern ray tracing systems. However, BVHs adapt poorly to non-uniformly tessellated scenes, which leads to increased ray shooting costs. This paper presents a novel and practical BVH construction algorithm, which addresses the issue by utilizing spatial splitting similar to kD-trees. In contrast to previous preprocessing approaches, our method uses the surface area heuristic to control primitive splitting during tree construction. We show that our algorithm produces significantly more efficient hierarchies than other techniques. In addition, user parameters that directly influence splitting are eliminated, making the algorithm easily controllable.
Overexpression of a Constitutively Active Protein Kinase G Mutant Reduces Neointima Formation and In-Stent Restenosis (2002)

Expression of a constitutively active PKG reduces neointima formation after balloon injury in rats and reduces coronary in-stent restenosis in pigs. PKGcat gene transfer may be a promising strategy for vasculoproliferative disorders.
Review of possible sources of exposure of horses to natural products and environmental contaminants resulting in regulatory action. (1997)

Natural products and environmental contaminants may be responsible for positive drug findings that result in regulatory actions against horse trainers. Knowledge of these potential sources of drugs may help horse trainers avoid sanctions. Author’s address: Analytical Toxicology Laboratory, College of Veterinary Medicine, The Ohio State University, 601 Vernon L. Tharp St., Columbus, OH 43210. r 1997 AAEP.
The Emergence of Thiol–Ene Coupling as a Click Process for Materials and Bioorganic Chemistry (2008)

The century-old thiol–ene radical reaction is now being recognized among the ranks of other click-type reactions (see scheme). Recent applications in dendrimer and glycopeptide syntheses demonstrate the efficiency of this process for the assembly of complex molecular systems.
GARP–TGF-β Complexes Negatively Regulate Regulatory T Cell Development and Maintenance of Peripheral CD4+ T Cells In Vivo (2013)

The role of surface-bound TGF-β on regulatory T cells (Tregs) and the mechanisms that mediate its functions are not well defined. We recently identified a cell-surface molecule called Glycoprotein A Repetitions Predominant (GARP), which is expressed specifically on activated Tregs and was found to bind latent TGF-β and mediate a portion of Treg suppressive activity in vitro. In this article, we address the role of GARP in regulating Treg and conventional T cell development and immune suppression in vivo using a transgenic mouse expressing GARP on all T cells. We found that, despite forced expression of GARP on all T cells, stimulation through the TCR was required for efficient localization of GARP to the cell surface. In addition, IL-2 signals enhanced GARP cell surface expression specifically on Tregs. GARP-transgenic CD4(+) T cells and Tregs, especially those expressing higher levels of GARP, were significantly reduced in the periphery. Mature Tregs, but not conventional CD4(+) T cells, were also reduced in the thymus. CD4(+) T cell reduction was more pronounced within the effector/memory subset, especially as the mouse aged. In addition, GARP-overexpressing CD4(+) T cells stimulated through the TCR displayed reduced proliferative capacity, which was restored by inhibiting TGF-β signaling. Furthermore, inhibiting TGF-β signals greatly enhanced surface expression of GARP on Tregs and blocked the induction of Foxp3 in activated CD4(+) T cells overexpressing GARP. These findings suggest a role for GARP in natural and induced Treg development through activation of bound latent TGF-β and signaling, which negatively regulates GARP expression on Tregs.
Identification of Antimicrobial Targets Using a Comprehensive Genomic Approach (2004)

Regulated antisense RNA enables the construction of a defined set of conditional growth-defective/lethal strains. In this study, we expanded the regulated antisense RNA interference technology and developed a high-throughput screening strategy to identify the potential drug targets of novel antimicrobials. To prove this concept, the specific antisense sublibrary of different essential open reading frames were pooled in the presence of an inducer, and treated with or without sublethal levels of mupirocin, triclosan, or gentamicin. Antisense RNA-expressing strains that were sensitized for increased susceptibility to the antibiotics were selectively detected via DNA subtractive hybridization, microarray, and whole-cell analyses. No strain was identified as supersensitive to gentamicin because there was no target-specific antisense strain in this sublibrary. In contrast, strains expressing antisense to isoleucine tRNA synthetase (ileS) and enoyl-[acyl-carrier-protein] reductase (fabI) were specifically identified as having increased susceptibility to mupirocin and triclosan, respectively. These results demonstrated that ileS and fabI antisense strains showed significant increases of susceptibility only to their specific inhibitors. This data demonstrates that a regulated antisense RNA expression library provides an effective tool to assist in the identification of potential targets for novel antibacterial agents.
Er:YAG laser ablation of tissue: Effect of pulse duration and tissue type on thermal damage (1989)

The thermal damage caused by 2.94-micron Er:YAG laser ablation of skin, cornea, aorta, and bone was quantified. The zone of residual thermal damage produced by normal-spiking-mode pulses (pulse duration approximately 200 microseconds) and Q-switched pulses (pulse duration approximately 90 ns) was compared. Normal-spiking-mode pulses typically leave 10-50 microns of collagen damage at the smooth wall of the incisions; however, at the highest fluences (approximately 80J/cm2) tears were produced in cornea and aorta and as much as 100 microns of damaged collagen is found at the incision edge. Q-switched pulses caused less thermal damage, typically 5-10 microns of damage in all tissues.
The Gamma Interferon Receptor Is Required for the Protective Pulmonary Inflammatory Response toCryptococcus neoformans (2005)

Mice with a null deletion mutation in the gamma interferon (IFN-gamma) receptor gene were used to study the role of IFN-gamma responsiveness during experimental pulmonary cryptococcosis. Cryptococcus neoformans was inoculated intratracheally into mice lacking the IFN-gamma receptor gene (IFN-gammaR-/-) and into control mice (IFN-gammaR+/+). The numbers of CFU in lung, spleen, and brain were determined to assess clearance; cytokines produced by lung leukocytes were measured, and survival curves were generated. In the present study, we demonstrate the following points. (i) IFN-gammaR-/- mice are markedly more susceptible to C. neoformans infection than IFN-gammaR+/+ mice. (ii) In the absence of IFN-gamma signaling, pulmonary CFU continue to increase over the course of infection, and the infection disseminates to the brain. (iii) In the absence of IFN-gamma receptor, recruitment of inflammatory cells in response to pulmonary cryptococcal infection is not impaired. (iv) At week 5 postinfection, IFN-gammaR-/- mice have recruited greater numbers of leukocytes into their lungs, with neutrophils, eosinophils, and lymphocytes accounting for this cellular increase. (v) IFN-gamma signaling is required for the development of a T1 over a T2 immune response in the lung following cryptococcal infection. These results indicate that in the absence of IFN- gamma responsiveness, even though the recruitment of pulmonary inflammatory cells is not impaired and the secretion of IFN-gamma is not affected, IFN-gammaR-/- mice do not have the ability to resolve the cryptococcal infection. In conclusion, our data suggest that proper functional IFN-gamma signaling, possibly through a mechanism which inhibits the potentially disease-promoting T2 response, is required for mice to confine the cryptococcal infection.
Mechanical properties and Raman spectra of tetrahedral amorphous carbon films with high sp3 fraction deposited using a filtered cathodic arc (1997)

Abstract The mechanical and structural properties of the tetrahedral amorphous carbon (ta-C) films deposited by the filtered cathodic vacuum arc technique on silicon at room temperature have been studied over the carbon ion energy range 15–200 eV. High (about 80% or higher) sp3 bond fractions were obtained for almost all ion energies investigated (E > 50 eV), with a maximum of about 87% at about 95 eV. The variations in the mechanical properties have been correlated to the sp3 fraction and show an almost linear dependence on the small variation in sp3 content. The maximum hardness, Young's modulus, stress critical load and minimum friction coefficient all coincide with the highest sp3 fraction as determined by electron-energy-loss spectroscopy. All films are atomically smooth. The Raman spectra of these films when fitted with a skewed Lorentzian, a parameter Q, which measures the degree of skewness, is noticeably dependent on films with sp2 content below 30% and can also be used to verify the ion energy corresponding to the maximum sp3 content. The change observed in the mechanical properties as well as the skewness parameter Q is attributed to a change in the local ordering of the sp2 bonded atoms in the ta-C sp3 matrix.
Novel Anticancer Agents in Clinical Development (2003)

There are currently more than 100 agents officially approved for the treatment of cancer world-wide. However, the most common epithelial cancers, which cause greater than 75% of cancer deaths, remain incurable. Most therapeutic agents have been developed empirically by testing large numbers of chemicals on rapidly growing transplantable rodent tumors, and more recently, human tumor xenografts. This approach has predominantly identified DNA-active drugs, which have limited efficacy and considerable toxicity. Novel agents, which selectively target aberrant elements in neoplastic cells and their microenvironment, are needed to improve the cure rates of epithelial malignancies. In recent years, advances in the understanding of molecular genetics and tumor biology have elucidated the molecular pathways implicated in the pathogenesis and progression of cancers and resulted in the discovery of a variety of novel molecular targets for therapeutic intervention. These targets can be conceptualized as supportive vessels, connective tissues, and signaling elements. Agents directed against these targets are those that interfere with signal transduction pathways, cell cycle regulation, and apoptosis (signals), malignant angiogenesis (vessels) and the tumor stroma (connective tissue). As anti-cancer therapeutics with distinct targeting capabilities against malignant cells become available for clinical evaluations, prioritization of these therapies for efficient allotment of clinical trial resources, identification of patients whose malignancies most likely express the molecular constituents resembling the true target, and derivation of relevant endpoints for both screening and assessment of clinical relevance will be critical to their ultimate development and success. This review will highlight promising rationally designed, target-based agents in clinical development, as well as the unique challenges involved in their successful development.
Expression of phagocyte NADPH oxidase components in human endothelial cells (1996)

Low-level generation of reactive oxygen species (ROS) by endothelial cells in response to a variety of stimuli has been observed; however, the enzyme system responsible is unknown. Using a variety of techniques, we examined for components of the phagocyte superoxide-generating NADPH oxidase to elucidate whether this enzyme could be a source of endothelial-derived ROS. Superoxide generation on addition of 100 microM NAD(P)H to human umbilical vein endothelial cell (HUVEC) sonicates (using lucigenin-enhanced chemiluminescence) was partially inhibited on addition of the flavoenzyme inhibitor diphenyliodonium (IDP). Reverse transcriptase-polymerase chain reaction (RT-PCR) demonstrated expression of gp91phox, p22phox, p67phox, and p47phox in four independent HUVEC isolates. Expression of p22phox was also confirmed by Northern blotting. RT-PCR for tumor necrosis factor-alpha was negative, indicating an absence of mononuclear cell contamination (a potential source of NADPH oxidase). Immunoperoxidase staining, using anti-p47phox (JW-1)- and anti-p67phox (JW-2)-specific antibodies, showed protein expression of these cytosolic components. However, heme spectroscopy failed to indicate the presence of the low-potential cytochrome b558. These data indicate that cultured human endothelial cells express both mRNA and protein for cytosolic components of the phagocyte superoxide-generating NADPH oxidase. However, because the cytochrome b558 heme could not be conclusively demonstrated, a contribution of the phagocyte NADPH oxidase to endothelial oxidant generation may be unlikely.
Portal hypertension associated with anticardiolipin antibodies in a case of systemic lupus erythematosus (1995)

A 26-year-old man with systemic lupus erythematosus (SLE) and a history of acute myocardial infarction developed portal hypertension accompanied by abnormal liver function and esophageal varices. As his clinical course suggested the possibility of antiphospholipid syndrome, a titer of anticardiolipin antibody (aCL) was serially measured using an enzyme immunoassay with beta 2-glycoprotein I as a cofactor. The titer of aCL increased with the development of portal hypertension, and promptly decreased with the improvement of liver function just after corticosteroid therapy. The long-term course in this case suggests that aCL may cause portal hypertension associated with SLE.
Integrin-Binding Peptides Derived from Phage Display Libraries (2003)

Integrins are a family of cell-surface receptors that recognize extracellular matrix proteins and mediate cell adhesion. Certain integrins bind to proteins containing the sequence Arg-Gly-Asp (RGD; ref. ). Such RGD-binding integrins include α5β1, αvβ3, αvβ5 and αIIbβ3 (,). Peptide libraries displayed on filamentous phage have provided a straightforward method to characterize the peptide-binding specificity of these integrins. In phage display-based strategies, libraries of random peptides are expressed on the surface of bacteriophage. Each individual phage carries a single peptide. The peptide is fused to the phage capsid protein pIII by insertion of its encoding DNA sequence in the pIII gene of the phage genome. Libraries displaying peptides fused to the major capsid protein pVIII have also been used. Libraries using the pIII protein display 3–5 copies of each individual peptide whereas libraries using the pVIII protein display approx 3000 copies (,). Analysis of the phage-displayed peptides found during screenings on purified integrins revealed that the majority of the integrin-binding peptides contain an RGD motif (, , , , , ). Other interesting ligand motifs were also found in the remaining population of integrin-binding peptides. Conversely, panning on immobilized fibronectin fragments containing the RGD sequence revealed peptide motifs present within integrins (). We describe here strategies for the use of phage display libraries in cell-adhesion research, with emphasis on the peptide-binding specificity of different members of the integrin family.
Fabrication of Polymeric Multimode Waveguides and Devices in SU-8 Photoresist Using Selective Polymerization. (2002)

Large cross section multimode waveguides have been realized in SU-8 using selective polymerization. SU-8 is a negative photoresist, which has shown good optical properties and it is mechanically and chemically stable. The fabricated waveguides have very smooth sidewalls and exhibit low optical losses. The fabrication method is simple and potentially very cost effective. N x N and 1 x N multimode power splitters have been realized using this fabrication technology.
Accumulation of Phosphorylated Repressor for Gibberellin Signaling in an F-box Mutant (2003)

Gibberellin (GA) regulates growth and development in plants. We isolated and characterized a rice GA-insensitive dwarf mutant, gid2. The GID2 gene encodes a putative F-box protein, which interacted with the rice Skp1 homolog in a yeast two-hybrid assay. In gid2, a repressor for GA signaling, SLR1, was highly accumulated in a phosphorylated form and GA increased its concentration, whereas SLR1 was rapidly degraded by GA through ubiquitination in the wild type. We conclude that GID2 is a positive regulator of GA signaling and that regulated degradation of SLR1 is initiated through GA-dependent phosphorylation and finalized by an SCF(GID2)-proteasome pathway.
In vivo lipid‐derived free radical formation by NADPH oxidase in acute lung injury induced by lipopolysaccharide: a model for ARDS (2002)

Intratracheal instillation of lipopolysaccharide (LPS) activates alveolar macrophages and infiltration of neutrophils, causing lung injury/acute respiratory distress syndrome. Free radicals are a special focus as the final causative molecules in the pathogenesis of lung injury caused by LPS. Although in vitro investigation has demonstrated radical generation after exposure of cells to LPS, in vivo evidence is lacking. Using electron spin resonance (ESR) and the spin trap alpha-(4-pyridyl-1-oxide)-N-tert-butylnitrone (POBN), we investigated in vivo free radical production by rats treated with intratracheal instillation of LPS. ESR spectroscopy of lipid extract from lungs exposed to LPS for 6 h gave a spectrum consistent with that of a POBN/carbon-centered radical adduct (aN=14.94+/-0.07 G and abetaH=2.42+/-0.06 G) tentatively assigned as a product of lipid peroxidation. To further investigate the mechanism of LPS-initiated free radical generation, rats were pretreated with the phagocytic toxicant GdCl3, which significantly decreased the production of radical adducts with a corresponding decrease in neutrophil infiltration. NADPH oxidase knockout mice completely blocked phagocyte-mediated, ESR-detectable radical production in this model of acute lung injury. Rats treated intratracheally with LPS generate lipid-derived free radicals via activation of NADPH oxidase.
Intelligent access to digital video: Informedia project (1996)

Carnegie Mellon's Informedia Digital Video Library project will establish a large, on-line digital video library featuring full-content and knowledge-based search and retrieval. Intelligent, automatic mechanisms will be developed to populate the library. Search and retrieval from digital video, audio, and text libraries will take place via desktop computer over local, metropolitan, and wide-area networks. The project's approach applies several techniques for content-based searching and video-sequence retrieval. Content is conveyed in both the narrative (speech and language) and the image. Only by the collaborative interaction of image, speech, and natural language understanding technology is it possible to successfully populate, segment, index, and search diverse video collections with satisfactory recall and precision. This collaborative interaction approach uniquely compensates for problems of interpretation and search in error-ridden and ambiguous data sets. The authors have focused the work on two corpuses. One is science documentaries and lectures, the other is broadcast news content with partial closed-captions. Further work will continue to improve the accuracy and performance of the underlying processing as well as explore performance issues related to Web-based access and interoperability with other digital video resources.
Near-infrared transillumination at 1310-nm for the imaging of early dental decay (2003)

New imaging technologies are needed for the early detection of dental caries (decay) in the interproximal contact sites between teeth. Previous measurements have demonstrated that dental enamel is highly transparent in the near-IR at 1300-nm. In this study, a near-IR imaging system operating at 1300-nm was used to acquire images through tooth sections of varying thickness and whole teeth in order to demonstrate the utility of a near-IR dental transillumination system for the imaging of early dental caries (decay). Simulated lesions, which model the optical scattering of natural dental caries, were placed in plano-parallel dental enamel sections. The contrast ratio between the simulated lesions and surrounding sound enamel was calculated from analysis of acquired projection images. The results show significant contrast between the lesion and the enamel (>0.35) and a spatial line profile that clearly resolves the lesion in samples as thick as 6.75-mm. This study clearly demonstrates that a near-IR transillumination system has considerable potential for the imaging of early dental decay.
Literature (2001)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation Roberta Hill, Karenne Wood, Colerus, Rawdon Tomlinson, Mike Catalano, Joan Wiese Johannes; Literature. American Indian Culture and Research Journal 1 January 2001; 25 (2): 137–155. doi: https://doi.org/10.17953/aicr.25.2.p71r880ljrh32885 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest Search
Deep Watershed Transform for Instance Segmentation (2016)

Most contemporary approaches to instance segmentation use complex pipelines involving conditional random fields, recurrent neural networks, object proposals, or template matching schemes. In our paper, we present a simple yet powerful end-to-end convolutional neural network to tackle this task. Our approach combines intuitions from the classical watershed transform and modern deep learning to produce an energy map of the image where object instances are unambiguously represented as basins in the energy map. We then perform a cut at a single energy level to directly yield connected components corresponding to object instances. Our model more than doubles the performance of the state-of-the-art on the challenging Cityscapes Instance Level Segmentation task.