gebhart/patrepeval huggingface dataset:
Acute, Sublethal, Antifeedant, and Synergistic Effects of Monoterpenoid Essential Oil Compounds on the Tobacco Cutworm, Spodoptera litura (Lep., Noctuidae) (2001)

Monoterpenoids (terpenes and biogenically related phenols) commonly found in plant essential oils were tested for acute toxicity via topical application to tobacco cutworms (Spodoptera litura Fab.). The most toxic among 10 such compounds was thymol (LD(50) = 25.4 microg/larva) from garden thyme, Thymus vulgaris. The compounds were then tested for sublethal effects, specifically inhibition of larval growth after topical application of low doses. Among 6 compounds tested, an LD(10) dose reduced growth by 20% on average 3 days after administration. Feeding deterrence was determined using a cabbage leaf disk choice test. The most deterrent compound was thymol, with a DC(50) of 85.6 microg/cm(2) leaf disk area. Because minor constituents in complex essential oils have been suggested to act as synergists, binary mixtures of the compounds were tested for synergy vis à vis acute toxicity and feeding deterrence. trans-Anethole acted synergistically with thymol, citronellal, and alpha-terpineol, in terms of both acute toxicity and feeding deterrence. On the basis of these findings, several complex mixtures were developed and tested as leads for effective control agents. Candidate mixtures demonstrated good synergistic effects. The observed LD(50) of mixture 3 was 40.6 microg/larvae compared to an expected value of 74.6 microg/larvae. The result of this research is a proprietary product suitable for commercial production.
Association of β-Arrestin with G Protein-coupled Receptors during Clathrin-mediated Endocytosis Dictates the Profile of Receptor Resensitization (1999)

Resensitization of G protein-coupled receptors (GPCRs) following agonist-mediated desensitization is a necessary step for maintaining physiological responsiveness. However, the molecular mechanisms governing the nature of GPCR resensitization are poorly understood. Here, we examine the role of beta-arrestin in the resensitization of the beta(2) adrenergic receptor (beta(2)AR), known to recycle and resensitize rapidly, and the vasopressin V2 receptor (V2R), known to recycle and resensitize slowly. Upon agonist activation, both receptors recruit beta-arrestin to the plasma membrane and internalize in a beta-arrestin- and clathrin-dependent manner. However, whereas beta-arrestin dissociates from the beta(2)AR at the plasma membrane, it internalizes with the V2R into endosomes. The differential trafficking of beta-arrestin and the ability of these two receptors to dephosphorylate, recycle, and resensitize is completely reversed when the carboxyl-terminal tails of these two receptors are switched. Moreover, the ability of beta-arrestin to remain associated with desensitized GPCRs during clathrin-mediated endocytosis is mediated by a specific cluster of phosphorylated serine residues in the receptor carboxyl-terminal tail. These results demonstrate that the interaction of beta-arrestin with a specific motif in the GPCR carboxyl-terminal tail dictates the rate of receptor dephosphorylation, recycling, and resensitization, and thus provide direct evidence for a novel mechanism by which beta-arrestins regulate the reestablishment of GPCR responsiveness.
Resources for Place Name Analysis (2004)

We present a new resource for annotating and visualizing the meaning of place names in natural language text, along with insights gained from analysis of manual annotations. The work addresses the issue of place name (toponym) meaning resolution, moving beyond simple named entity recognition to address the problem of grounding textual references, i.e., making a connection between the references and the real-world entities that they denote. The name, “San Francisco, ” for example, can be mapped to more than 900 distinct place entities that differ in terms of location and/or type, according to commonly available databases of named geographical entities, called gazetteers. Gazetteers serve as knowledge bases that can be exploited to support the analysis and disambiguation of named places, and the grounding of textual references in real-world entities. This process of grounding text in gazetteers offers a way of normalizing the meaning of the place name references that are found in the gazetteers, and essentially subsumes the text analysis process of determining when instances of a given name are being used to refer to the same or to different entities.
Synthesis of New Pseudodisaccharide Aminoglycoside Antibiotics from Carbohydrates. (1995)

Novel pseudodisaccharide-type aminocyclitol antibiotic models, built up from D-arabinose, D-ribose, D-glucosamine, L-ristosamine and L-acosamine have been synthesized by the glycosylation of suitably protected (azido)deoxyinosose aglycones derived by the Ferrier carbocyclic ring transformation of carbohydrate precursors. An alternative approach to related pseudodisaccharides, based on the Ferrier carbocyclization of reducing disaccharides, has also been elaborated. This latter method extends the scope of the Ferrier reaction, by demonstrating that acid-labile 2-deoxydisaccharides can also be readily transformed into the corresponding pseudodisaccharides under the slightly acidic conditions of this ring-transformation.
Immunochemical studies of human erythropoietin using site-specific anti-peptide antibodies. Identification of a functional domain. (1987)

Anti-peptide antibodies that bind to the amino terminus of human erythropoietin (residues 1-26) do not inhibit the hormone's biological activity, indicating that this region of the protein does not play a role in receptor recognition (Sytkowski, A. J., and Fisher, J. W. (1985) J. Biol Chem. 260, 14727-14731). We have now identified six other regions of the primary sequence that are relatively hydrophilic and, therefore, have a higher probability of being accessible to such antibody probes. Antibodies raised against synthetic peptides homologous to five of these regions, corresponding to residues 40-59, 80-99, 99-118, 111-129, and 131-150 recognize erythropoietin, confirming the prediction based upon relative hydrophilicity. Antibodies to a carboxyl terminal peptide 147-166 failed to bind the hormone, presumably due to steric hindrance imposed by a disulfide bond between Cys161 and one of the other cysteinyl residues. The antibodies were affinity purified on the relevant immobilized peptide and their capacity to inhibit (neutralize) erythropoietin's activity was assessed. Only anti-peptide 99-118 and anti-peptide 111-129 antibodies inhibited erythropoietin. This effect was reversed by excess peptide, demonstrating that the neutralizing action of the antibody was due to its antigen-specific binding. The results strongly suggest that the portion of erythropoietin's amino acid sequence represented by these peptides plays a functional role in the hormone's action, most probably by forming part of the receptor-binding domain.
A Novel Role of Dipeptidyl Peptidase 9 in Epidermal Growth Factor Signaling (2011)

Dipeptidyl peptidase IV (DPP4), DPP8, DPP9, and fibroblast activation protein (FAP), the four proteases of the DPP4 gene family, have unique peptidase and extra-enzymatic activities that have been implicated in various diseases including cancers. We report here a novel role of DPP9 in regulating cell survival and proliferation through modulating molecular signaling cascades. Akt (protein kinase B) activation was significantly inhibited by human DPP9 overexpression in human hepatoma cells (HepG2 and Huh7) and human embryonic kidney cells (HEK293T), whereas extracellular signal-regulated kinases (ERK1/2) activity was unaffected, revealing a pathway-specific effect. Interestingly, the inhibitory effect of DPP9 on Akt pathway activation was growth factor dependent. DPP9 overexpression caused apoptosis and significantly less epidermal growth factor (EGF)-mediated Akt activation in HepG2 cells. However, such inhibitory effect was not observed in cells stimulated with other growth factors, including connective tissue growth factor, hepatic growth factor, insulin or platelet-derived growth factor-BB. The effect of DPP9 on Akt did not occur when DPP9 enzyme activity was ablated by either mutagenesis or inhibition. The phosphatidylinositol 3-kinase (PI3K)/Akt pathway is a major downstream effector of Ras. We found that DPP9 and DPP8, but not DPP4 or FAP, associate with H-Ras, a key signal molecule of the EGF receptor signaling pathway. These findings suggest an important signaling role of DPP9 in the regulation of survival and proliferation pathways.
A Blocking Anti-CD28-Specific Antibody Induces Long-Term Heart Allograft Survival by Suppression of the PKCθ-JNK Signal Pathway (2008)

This study investigated the effects of a blocking anti-CD28 antibody (Anti-CD28-PV1-IgG3) in vitro and in vivo. Anti-CD28-PV1-IgG3, a hamster-mouse chimeric antibody against murine CD28, which does not provide CD28-positive signaling during TCR-driven T cell activation, enabled long-term survival of heart allografts across a complete mismatch of the MHC in rats. Among the T cell signaling proteins tested in the spleens from recipients, we found that recipients treated with anti-CD28-PV1-IgG3 exhibited suppression of alloantigen-initiated proximal TCR signaling events, including Lck, Zap70, Vav, and PI3K expression, and their PKC theta- and JNK-regulated expression/activation. This leads to attenuation of intragraft T cell infiltration and expression of T cell effector molecules. These results indicate that targeting the CD28 receptor with a blocking antibody leads to long-term allograft survival by reducing activation of alloantigen-mediated key signaling events in T cells that might be crucial for full T cell activation.
NF-κB regulation of endothelial cell function during LPS-induced toxemia and cancer (2006)

The transcription factor NF-kappaB is an important regulator of homeostatic growth and inflammation. Although gene-targeting studies have revealed important roles for NF-kappaB, they have been complicated by component redundancy and lethal phenotypes. To examine the role of NF-kappaB in endothelial tissues, Tie2 promoter/enhancer-IkappaBalpha(S32A/S36A) transgenic mice were generated. These mice grew normally but exhibited enhanced sensitivity to LPS-induced toxemia, notable for an increase in vascular permeability and apoptosis. Moreover, B16-BL6 tumors grew significantly more aggressively in transgenic mice, underscoring a new role for NF-kappaB in the homeostatic response to cancer. Tumor vasculature in transgenic mice was extensive and disorganized. This correlated with a marked loss in tight junction formation and suggests that NF-kappaB plays an important role in the maintenance of vascular integrity and response to stress.
Rethinking virtual network embedding (2008)

Network virtualization is a powerful way to run multiple architectures or experiments simultaneously on a shared infrastructure. However, making efficient use of the underlying resources requires effective techniques for virtual network embedding--mapping each virtual network to specific nodes and links in the substrate network. Since the general embedding problem is computationally intractable, past research restricted the problem space to allow efficient solutions, or focused on designing heuristic algorithms. In this paper, we advocate a different approach: rethinking the design of the substrate network to enable simpler embedding algorithms and more efficient use of resources, without restricting the problem space. In particular, we simplify virtual link embedding by: i) allowing the substrate network to split a virtual link over multiple substrate paths and ii) employing path migration to periodically re-optimize the utilization of the substrate network. We also explore node-mapping algorithms that are customized to common classes of virtual-network topologies. Our simulation experiments show that path splitting, path migration,and customized embedding algorithms enable a substrate network to satisfy a much larger mix of virtual networks
Side Chain Bromination of 2- Methyl Naphthalene by an Electro Chemical Method (2018)

A simple method for the preparation of 2- Bromo Methyl Naphthalene from 2- Methyl Naphthalene is reported. The electrolysis was carried out in a divided electrochemical cell fitted with graphite electrode at 0°C. The conversion of 2- Methyl naphthalene varies from 70 to 75 % and the selectivity is observed 92%. The effects of different electrode, different solvent, and different current densities are studied and reported.
Realization of continuous Zachariasen carbon monolayer (2017)

Rapid progress in two-dimensional (2D) crystalline materials has recently enabled a range of device possibilities. These possibilities may be further expanded through the development of advanced 2D glass materials. Zachariasen carbon monolayer, a novel amorphous 2D carbon allotrope, was successfully synthesized on germanium surface. The one-atom-thick continuous amorphous layer, in which the in-plane carbon network was fully <i>sp</i><sup>2</sup>-hybridized, was achieved at high temperatures (>900°C) and a controlled growth rate. We verified that the charge carriers within the Zachariasen carbon monolayer are strongly localized to display Anderson insulating behavior and a large negative magnetoresistance. This new 2D glass also exhibited a unique ability as an atom-thick interface layer, allowing the deposition of an atomically flat dielectric film. It can be adopted in conventional semiconductor and display processing or used in the fabrication of flexible devices consisting of thin inorganic layers.
Characterization of the Surface Activity of a Synthetic Surfactant with Albumin. (2002)

We previously reported that a human analogue of pulmonary surfactant protein-C (SP-C), SP-CL16 (6-28), with 23 residues was the most active analogue in a reconstituted lipid mixture and had the shortest chain among the poly leucine analogues examined. In this study, we verified the influence of albumin, a component of serum, on the surface activity of surfactant. Surface activity was measured using the Langmuir-Wilhelmy surface balance (WSB), pulsating bubble surfactometer (PBS), and stable microbubble test (MBT). The surface activity of synthetic lung surfactant (SLS) was only slightly influenced by albumin (0.1-10 mg/ml) as compared with that of a ternary mixture of phospholipids. The ternary mixture of phospholipids showed a decrease in surface activity due to albumin. In particular, SLS did not show interaction of surface activity with albumin in vitro (WSB, PBS, and MBT). In contrast, dipalmitoylphosphatidylcholine/phosphatidylglycerol/palmitic acid had significantly weaker surface activity in the presence of albumin. Surfactant-TA showed interaction of surface activity with albumin in the MBT. The number of stable microbubble increased in the presence of albumin at a concentration of 0.1 mg/ml.
End-to-End eScience: Integrating Workflow, Query, Visualization, and Provenance at an Ocean Observatory (2008)

Data analysis tasks at an Ocean Observatory require integrative and and domain-specialized use of database, workflow, visualization systems. We describe a platform to support these tasks developed as part of the cyberinfrastructure at the NSF Science and Technology Center for Coastal Margin Observation and Prediction integrating a provenance-aware workflow system, 3D visualization, and a remote query engine for large-scale ocean circulation models. We show how these disparate tools complement each other and give examples of real scientific insights delivered by the integrated system. We conclude that data management solutions for eScience require this kind of holistic, integrative approach, explain how our approach may be generalized, and recommend a broader, application-oriented research agenda to explore relevant architectures.
Targeted siRNA Delivery and mRNA Knockdown Mediated by Bispecific Digoxigenin-binding Antibodies (2012)

Bispecific antibodies (bsAbs) that bind to cell surface antigens and to digoxigenin (Dig) were used for targeted small interfering RNA (siRNA) delivery. They are derivatives of immunoglobulins G (IgGs) that bind tumor antigens, such as Her2, IGF1-R, CD22, and LeY, with stabilized Dig-binding variable domains fused to the C-terminal ends of the heavy chains. siRNA that was digoxigeninylated at its 3'end was bound in a 2:1 ratio to the bsAbs. These bsAb-siRNA complexes delivered siRNAs specifically to cells that express the corresponding antigen as demonstrated by flow cytometry and confocal microscopy. The complexes internalized into endosomes and Dig-siRNAs separated from bsAbs, but Dig-siRNA was not released into the cytoplasm; bsAb-targeting alone was thus not sufficient for effective mRNA knockdown. This limitation was overcome by formulating the Dig-siRNA into nanoparticles consisting of dynamic polyconjugates (DPCs) or into lipid-based nanoparticles (LNPs). The resulting complexes enabled bsAb-targeted siRNA-specific messenger RNA (mRNA) knockdown with IC(50) siRNA values in the low nanomolar range for a variety of bsAbs, siRNAs, and target cells. Furthermore, pilot studies in mice bearing tumor xenografts indicated mRNA knockdown in endothelial cells following systemic co-administration of bsAbs and siRNA formulated in LNPs that were targeted to the tumor vasculature.Molecular Therapy - Nucleic Acids (2012) 1, e45; doi:10.1038/mtna.2012.39; published online 18 September 2012.
Automated discovery of 3D motifs for protein function annotation (2006)

Supplementary data are available at Bioinformatics online.
Keynote talk: Experiences with MapReduce, an abstraction for large-scale computation (2006)

MapReduce is a programming model and an associated implementation for processing and generating large data sets. Users specify a Map function that processes a key/value pair to generate a set of intermediate key/value pairs, and a Reduce function that merges all intermediate values associated with the same intermediate key. Many real world tasks are expressible in this model. Programs written in this functional style are automatically parallelized and executed on a large cluster of commodity machines. The MapReduce run-time system takes care of the details of partitioning the input data, scheduling the program's execution across a set of machines, handling machine failures, and managing the required inter-machine communication. This allows programmers without any experience with parallel and distributed systems to easily utilize the resources of a large distributed system. Our implementation of MapReduce runs on a large cluster of commodity machines and is highly scalable: a typical MapReduce computation processes many terabytes of data on thousands of machines. Programmers find the system easy to use: thousands of MapReduce programs have been implemented and several thousand thousand MapReduce jobs are executed on Google's clusters every day. In this talk I'll describe the basic programming model, discuss our experience using it in a variety of domains, and talk about the implications of programming models like MapReduce as one paradigm to simplify development of parallel software for multi-core microprocessors.
Cerebellar Volume in Adults With Down Syndrome (1997)

Although cerebellar volumes are disproportionately small in individuals with DS, they do not diminish significantly with age and do not undergo age-related atrophy that is different from that of normal controls. Volume reduction in the cerebellum does not appear to be specifically responsible for the age-related decline in fine-motor control that is observed in adults with DS.
The classical pathway is the dominant complement pathway required for innate immunity toStreptococcus pneumoniaeinfection in mice (2002)

The complement system is an important component of the innate immune response to bacterial pathogens, including Streptococcus pneumoniae . The classical complement pathway is activated by antibody–antigen complexes on the bacterial surface and has been considered predominately to be an effector of the adaptive immune response, whereas the alternative and mannose-binding lectin pathways are activated directly by bacterial cell surface components and are considered effectors of the innate immune response. Recently, a role has been suggested for the classical pathway during innate immunity that is activated by natural IgM or components of the acute-phase response bound to bacterial pathogens. However, the functional importance of the classical pathway for innate immunity to S. pneumoniae and other bacterial pathogens, and its relative contribution compared with the alternative and mannose-binding lectin pathways has not been defined. By using strains of mice with genetic deficiencies of complement components and secretory IgM we have investigated the role of each complement pathway and natural IgM for innate immunity to S. pneumoniae . Our results show that the proportion of a population of S. pneumoniae bound by C3 depends mainly on the classical pathway, whereas the intensity of C3 binding depends on the alternative pathway. Furthermore, the classical pathway, partially targeted by the binding of natural IgM to bacteria, is the dominant pathway for activation of the complement system during innate immunity to S. pneumoniae , loss of which results in rapidly progressing septicemia and impaired macrophage activation. These data demonstrate the vital role of the classical pathway for innate immunity to a bacterial pathogen.
<title>Metalized polyimide filters for x-ray astronomy and other applications</title> (1997)

Filters fabricated from metalized polyimide have been specified for a number of x-ray astronomy missions, including the Advanced X-ray Astrophysics Facility (AXAF), the x-ray spectrometer (XRS) on Astro-E, the Advanced Composition Explorer (ACE), and the Geostationary Operational Environmental Satellite (GOES). Polyimide offers greater strength, improved temperature stability, and effectiveness in blocking unwanted ultraviolet radiation compared to polymeric films previously employed. This paper reviews the various x- ray astronomy missions and the particular challenges that were met with polyimide filters. The paper also reviews the development of free standing thin foils of polyimide with mechanical properties optimized for x-ray astronomy and other applications, such as synchrotron research.
Structural characterization of amorphous calcium carbonate-binding protein: an insight into the mechanism of amorphous calcium carbonate formation (2013)

ACC (amorphous calcium carbonate) plays an important role in biomineralization process for its function as a precursor for calcium carbonate biominerals. However, it is unclear how biomacromolecules regulate the formation of ACC precursor in vivo. In the present study, we used biochemical experiments coupled with bioinformatics approaches to explore the mechanisms of ACC formation controlled by ACCBP (ACC-binding protein). Size-exclusion chromatography, chemical cross-linking experiments and negative staining electron microscopy reveal that ACCBP is a decamer composed of two adjacent pentamers. Sequence analyses and fluorescence quenching results indicate that ACCBP contains two Ca²⁺-binding sites. The results of in vitro crystallization experiments suggest that one Ca²⁺-binding site is critical for ACC formation and the other site affects the ACC induction efficiency. Homology modelling demonstrates that the Ca²⁺-binding sites of pentameric ACCBP are arranged in a 5-fold symmetry, which is the structural basis for ACC formation. To the best of our knowledge, this is the first report on the structural basis for protein-induced ACC formation and it will significantly improve our understanding of the amorphous precursor pathway.