gebhart/patrepeval huggingface dataset:
C-Terminal Region of Dengue Virus Nonstructural Protein 1 Is Involved in Endothelial Cell Cross-Reactivity via Molecular Mimicry (2008)

Infection with dengue virus (DV) causes diseases ranging from self-limited dengue fever to life-threatening dengue hemorrhagic fever and dengue shock syndrome. Vascular leakage, thrombocytopenia and bleeding are the clinical manifestations associated with dengue hemorrhage. We previously showed that anti-DV nonstructural protein 1 (NS1) antibodies (Abs) cross-reacted with endothelial cells. The potential target proteins on endothelial cell surface recognized by anti-DV NS1 Abs showed sequence homology with the C-terminal amino acids (a.a.) 311-352 of DV NS1. In this study, the role of NS1 C-terminal region in dengue autoimmunity was investigated. We deleted the a.a. 277-352 of DV NS1 to prepare truncated NS1 (tNS1) and generated anti-DV tNS1 Abs in mice. The endothelial cell-binding activity of anti-DV tNS1 Abs was lower than that of anti-DV NS1 Abs. In addition, the endothelial cell-binding activity of anti-DV NS1 Abs was inhibited by preabsorption with DV NS1 but not with DV tNS1 proteins. The anti-P311 (a.a. 311-330) and anti-P331 (a.a. 331-350) titers of dengue patient sera were positively correlated with their endothelial cell-binding activity. Dengue patient sera showed lower binding activity to DV tNS1 than to DV NS1 proteins. The endothelial cell-binding activity of dengue patient sera was inhibited by preabsorption with P311 and P331. This study helps to understand the molecular mechanisms of autoimmunity mediated by anti-DV NS1 Abs and to provide the potential implications of tNS1 in dengue vaccine strategies.
Permissive glycan support of photoreceptor outer segment assembly occurs via a non-metabolic mechanism. (2003)

The ability of both lactose and IPTG to support outer segment assembly in the absence of the RPE is dose-dependent and the effect of these sugars upon membrane folding is reversible. Moreover, this effect is supported by a non-metabolic mechanism and is therefore not accounted for by simple provision of an energy source.
Regular papers Specifying and executing behavioral requirements: the play-in/play-out approach (2003)

Abstract. A powerful methodology for scenario-based specification of reactive systems is described, in which the behavior is “played in ” directly from the system’s GUI or some abstract version thereof, and can then be “played out”. The approach is supported and illustrated by a tool, which we call the play-engine. As the behavior is played in, the play-engine automatically generates a formal version in an extended version of the language of live sequence charts (LSCs). As they are played out, it causes the application to react according to the universal (“must”) parts of the specification; the existential (“may”) parts can be monitored to check their successful completion. Play-in is a user-friendly high-level way of specifying behavior and play-out is a rather surprising way of working with a fully operational system directly from its inter-object requirements. The ideas appear to be relevant to many stages of system development, including requirements engineering, specification, testing, analysis and implementation.
Method for fabricating submicron silicide structures on silicon using a resistless electron beam lithography process (1997)

A novel resistless lithography process using a conventional electron beam system is presented. Metallic lines with widths of less than 50 nm were produced on silicon substrates. The process is based on localized heating with a focused electron beam of thin platinum layers deposited on silicon. It is demonstrated that silicide formation occurs at the Pt-Si interface. By using a dilute solution of aqua regia, it is possible to obtain a sufficient difference in etch rates between exposed and unexposed regions of the platinum thin film to selectively remove only the unexposed areas.
Mid-infrared distributed-feedback interband cascade lasers with continuous-wave single-mode emission to 80 °C (2012)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation C. S. Kim, M. Kim, J. Abell, W. W. Bewley, C. D. Merritt, C. L. Canedy, I. Vurgaftman, J. R. Meyer; Mid-infrared distributed-feedback interband cascade lasers with continuous-wave single-mode emission to 80 °C. Appl. Phys. Lett. 6 August 2012; 101 (6): 061104. https://doi.org/10.1063/1.4744445 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 filter your search All ContentAIP Publishing PortfolioApplied Physics Letters Search Advanced Search |Citation Search
Design, Synthesis, and Biological Evaluation of New 8-Heterocyclic Xanthine Derivatives as Highly Potent and Selective Human A<sub>2B</sub>Adenosine Receptor Antagonists (2004)

Here we report the synthesis of 8-heterocycle-substituted xanthines as potent and selective A(2B) adenosine receptor antagonists. The structure-activity relationships (SAR) of the xanthines synthesized in binding to recombinant human A(2B) adenosine receptors (ARs) in HEK-293 cells (HEK-A(2B)) and at other AR subtypes were explored. The synthesized compounds showed A(2B) adenosine receptor affinity in the nanomolar range and good levels of selectivity evaluated in radioligand binding assays at human (h) A(1), A(2A), A(2B), and A(3) ARs. We introduced several heterocycles, such as pyrazole, isoxazole, pyridine, and pyridazine, at the 8-position of the xanthine nucleus and we have also investigated different spacers (substituted acetamide, oxyacetamide, and urea moieties) on the heterocycle introduced. Various groups at the 3- and 4-positions of phenylacetamide moiety were studied. This study allowed us to identify the derivatives 2-(3,4-dimethoxyphenyl)-N-[5-(2,6-dioxo-1,3-dipropyl-2,3,6,7-tetrahydro-1H-purin-8-yl)-1-methyl-1H-pyrazol-3-yl]acetamide (29b, MRE2028F20) [K(i)(hA(2B)) = 38 nM, K(i)(hA(1),hA(2A),hA(3)) >1000 nM], N-benzo[1,3]dioxol-5-yl-2-[5-(2,6-dioxo-1,3-dipropyl-2,3,6,7-tetrahydro-1H-purin-8-yl)-1-methyl-1H-pyrazol-3-yloxy]acetamide (62b, MRE2029F20) [K(i)(hA(2B)) = 5.5 nM, K(i)(hA(1),hA(2A),hA(3)) > 1000 nM], and N-(3,4-dimethoxyphenyl)-2-[5-(2,6-dioxo-1,3-dipropyl-2,3,6,7-tetrahydro-1H-purin-8-yl)-1-methyl-1H-pyrazol-3-yloxy]acetamide (72b, MRE2030F20) [K(i)(hA(2B) = 12 nM, K(i)(hA(1),hA(2A), hA(3)) > 1000 nM], which showed high affinity at the A(2B) receptor subtype and very good selectivity vs the other ARs. Substitution of the acetamide with an urea moiety afforded bioisosteric xanthines with good affinity and selectivity comparable to the acetamide derivatives. Substitution at the para-position of a 4-benzyloxy group of the phenylacetamido chain enhanced affinity at the A(2B) receptor [compound 30b (K(i)(hA(2B)) = 13 nM) vs compound 21b (K(i)(hA(2B) = 56 nM)] but did not favor selectivity. The derivatives with higher affinity at human A(2B) AR proved to be antagonists, in the cyclic AMP assay, capable of inhibiting the stimulatory effect of NECA (100 nM) with IC(50) values in the nanomolar range, a trend similar to that observed in the binding assay (62b, IC(50) = 38 nM; 72b, IC(50) = 46 nM). In conclusion, the 8-pyrazolo-1,3-dipropyl-1H-purine-2,6-dione derivatives described herein represent a new family of selective antagonists for the adenosine A(2B) receptor.
Automated Essay Scoring (2003)

This new volume is the first to focus entirely on automated essay scoring and evaluation. It is intended to provide a comprehensive overview of the evolution and state-of-the-art of automated essay scoring and evaluation technology across several disciplines, including education, testing and measurement, cognitive science, computer science, and computational linguistics. The development of this technology has led to many questions and concerns. Automated Essay Scoring attempts to address some of these questions including: *How can automated scoring and evaluation supplement classroom instruction? *How does the technology actually work? *Can it improve students' writing? *How reliable is the technology? *How can these computing methods be used to develop evaluation tools? *What are the state-of the-art essay evaluation technologies and automated scoring systems? Divided into four parts, the first part reviews the teaching of writing and how computers can contribute to it. Part II analyzes actual automated essay scorers including e-raterTM, Intellimetric, and the Intelligent Essay Assessor. The third part analyzes related psychometric issues, and the final part reviews innovations in the field. This book is ideal for researchers and advanced students interested in automated essay scoring from the fields of testing and measurement, education, cognitive science, language, and computational linguistics.
Developing new methods for the treatment of malignant brain tumours: local delivery of anti-neoplastic agents using biodegradable polymers. (2000)

Controlled delivery of chemotherapeutic agents by biodegradable polymers is a new strategy that has been added to the arsenal available for the treatment of malignant neoplasms. This approach is particularly suitable for the management of brain tumours because of the constraints imposed by the blood brain barrier (BBB). The use of polymers for local drug delivery minimises systemic toxicity, while achieving prolonged elevation of intratumoural drug concentrations that results in improved efficacy. In addition, this strategy broadens the spectrum of drugs available for the treatment of neoplasms in the central nervous system to include agents whose efficacy is significantly limited by systemic toxicity or inability to penetrate the BBB. In this review, we discuss the rationale and background for the use of this novel approach. We also summarise the clinical trials and laboratory investigations leading to the development of local delivery of anti-neoplastic agents from biodegradable polymers for the treatment of malignant gliomas.
Gene Expression Profiling (GEP) in Multiple Myeloma (MM): Comparison of Purified MM Cells (PMM), Random Bone Marrow Biopsies (RBX) and Fine Needle Biopsies from Focal Lesions (FNBX). (2005)

Abstract Background: GEP has become a useful tool for the distinction of genetic subgroups of patients with malignant disease of a common pathologic diagnosis, including MM. The aim of this study was to determine whether whole bone marrow biopsies could replace the laborious magnetic bead purification of CD 138-positive plasma cells, with the potential added advantages of: 1. less sample manipulation and thus facilitating shipping to a central processing and analysis facility; 2. encompassing the bone marrow micro-environment as an important contributor to MM survival and drug resistance. Patients and Methods: Samples included paired PMM and RBX from 190 newly diagnosed patients treated on Total Therapy protocols TT2 (n = 85) and TT3 (n = 105); 29 of these patients also had CT-guided fine needle biopsies (FNBX); 5 subjects with MGUS and 5 normal donors were used for comparison. Total RNA was applied to Affymetrix U133 Plus2 microarray chips. Unsupervised hierarchical clustering (UHC) was performed on Log2 transformed GEP intensity values of probe sets with &gt;95% present detection calls and &gt;0.5 standard deviation. Results: UHC analysis of RBX (MM, MGUS, normal) identified 2 major subgroups: one containing both normal and MGUS samples (“normal-like”, N-L) and the other comprising only MM samples (“myeloma-like”, M-L) (Figure 1). In the context of previously defined 7 GEP subgroups (Zhan et al, Blood 2004), the N-L group contained higher proportions of hyperdiploid and normal karyotype cases, whereas the M-L group comprised the majority of MAF/MAFB, FGFR3/MMSET and proliferation cases. Good-risk standard laboratory features (non-IgA isotype, lower B2M and CRP levels, higher Hb concentrations) were over-represented in the N-L group. When applied to TT2 patients with a median follow-up of 3 years, N-L patients had superior 3-yr EFS (85% vs 55% for M-L group; p=.02). A further UHC analysis addressed similarities/differences among PMM, RBX and FNBX samples available in 29 patients. The dendrogram had 2 major branches; one comprising all PMM samples and the other all BX with sub-branches separating RBX and FNBX subgroups. Finally, 90% of all MAF, MAFB, FGFR3, MMSET and CCND1 “spikes” identified in PMM (with well established prognostic implications) were also detectable in RBX and FNBX samples. Conclusion: GEP analysis of RBX distinguished 2 subgroups, M-L and N-L, in the context of comparison with normal subjects and MGUS. Compared to M-L, N-L patients (comprising more favorable genetic and standard laboratory features) had superior EFS. Both RBX and FNBX were adequate tissue sources for the detection of prognosis- and possibly therapy-relevant translocation-associated “spiked” genes. Genes differentiating PMM, RBX and FNBX will be reported at the meeting. BX as tissue source should make GEP studies of MM feasible in the context of multi-institutional trials.
A key-management scheme for distributed sensor networks (2002)

Distributed Sensor Networks (DSNs) are ad-hoc mobile networks that include sensor nodes with limited computation and communication capabilities. DSNs are dynamic in the sense that they allow addition and deletion of sensor nodes after deployment to grow the network or replace failing and unreliable nodes. DSNs may be deployed in hostile areas where communication is monitored and nodes are subject to capture and surreptitious use by an adversary. Hence DSNs require cryptographic protection of communications, sensor-capture detection, key revocation and sensor disabling. In this paper, we present a key-management scheme designed to satisfy both operational and security requirements of DSNs. The scheme includes selective distribution and revocation of keys to sensor nodes as well as node re-keying without substantial computation and communication capabilities. It relies on probabilistic key sharing among the nodes of a random graph and uses simple protocols for shared-key discovery and path-key establishment, and for key revocation, re-keying, and incremental addition of nodes. The security and network connectivity characteristics supported by the key-management scheme are discussed and simulation experiments presented.
CKAP4 is a Dickkopf1 receptor and is involved in tumor progression (2016)

Dickkopf1 (DKK1) is a secretory protein that antagonizes oncogenic Wnt signaling by binding to the Wnt coreceptor low-density lipoprotein receptor-related protein 6 (LRP6). DKK1 may also regulate its own signaling to promote cancer cell proliferation, but the mechanism is not understood. Here, we identified cytoskeleton-associated protein 4 (CKAP4) as a DKK1 receptor and evaluated CKAP4-mediated DKK1 signaling in cancer cell proliferation. We determined that DKK1 binds CKAP4 and LRP6 with similar affinity but interacts with these 2 receptors with different cysteine-rich domains. DKK1 induced internalization of CKAP4 in a clathrin-dependent manner, further supporting CKAP4 as a receptor for DKK1. DKK1/CKAP4 signaling activated AKT by forming a complex between the proline-rich domain of CKAP4 and the Src homology 3 domain of PI3K, resulting in proliferation of normal cells and cancer cells. Expression of DKK1 and CKAP4 was frequent in tumor lesions of human pancreatic and lung cancers, and simultaneous expression of both proteins in patient tumors was negatively correlated with prognosis and relapse-free survival. An anti-CKAP4 antibody blocked the binding of DKK1 to CKAP4, suppressed AKT activity in a human cancer cell line, and attenuated xenograft tumor formation in immunodeficient mice. Together, our results suggest that CKAP4 is a potential therapeutic target for cancers that express both DKK1 and CKAP4.
Consolidated bioprocessing of starchy substrates into ethanol by industrial <i>Saccharomyces cerevisiae</i> strains secreting fungal amylases (2015)

The development of a yeast strain that converts raw starch to ethanol in one step (called Consolidated Bioprocessing, CBP) could significantly reduce the commercial costs of starch-based bioethanol. An efficient amylolytic Saccharomyces cerevisiae strain suitable for industrial bioethanol production was developed in this study. Codon-optimized variants of the Thermomyces lanuginosus glucoamylase (TLG1) and Saccharomycopsis fibuligera α-amylase (SFA1) genes were δ-integrated into two S. cerevisiae yeast with promising industrial traits, i.e., strains M2n and MEL2. The recombinant M2n[TLG1-SFA1] and MEL2[TLG1-SFA1] yeast displayed high enzyme activities on soluble and raw starch (up to 8118 and 4461 nkat/g dry cell weight, respectively) and produced about 64 g/L ethanol from 200 g/L raw corn starch in a bioreactor, corresponding to 55% of the theoretical maximum ethanol yield (g of ethanol/g of available glucose equivalent). Their starch-to-ethanol conversion efficiencies were even higher on natural sorghum and triticale substrates (62 and 73% of the theoretical yield, respectively). This is the first report of direct ethanol production from natural starchy substrates (without any pre-treatment or commercial enzyme addition) using industrial yeast strains co-secreting both a glucoamylase and α-amylase.
Control and Optimization of Directional Drilling System (2015)

Abstract Directional Drilling (DD) achieves higher well production and improves accessibility of oil reservoirs in complex locations. Quad Motor drilling heads was recently proposed to achieve better steering control of the drilling operation and higher dogleg severity. The current state of the art in DD is the Rotary Steerable System (RSS), where steering actuators displace the centerline of the drilling system away from the centerline of the hole by a controllable amount of eccentricity. The drilling bit is powered by the rotation of the drilling string. However, in the quad motor drilling head, four drilling bits are independently controlled by 4 downhole motors. This paper proposes a real time control and optimization of the quad bit directional drilling system. The control commands include the angular velocity and torque of each of the 4 motors. The control is updated at regular distance intervals. The optimization procedure determines the drilling parameters to minimize the drilling time and the deviation from the planned trajectory.
Polarization and switching properties of holographic polymer-dispersed liquid-crystal gratings II Experimental investigations (2002)

We have performed a detailed study of the polarization properties and switching behavior of holographic polymer-dispersed liquid-crystal gratings. A theoretical model [ R. L. Sutherland , J. Opt. Soc. Am. B19, 2995 (2002)] is compared with a number of observed phenomena in reflection and transmission gratings made with different types of liquid crystals under a variety of experimental conditions. Anomalous polarization effects are described and interpreted. We show that a wide variation of holographic polymer-dispersed liquid-crystal grating properties can be explained in terms of the statistics of droplet orientational distributions.
A Kinetic and Mechanistic Study of the Low-Temperature Fluorine-Initiated Copolymerization of Tetrafluoroethylene with Oxygen (1999)

The fluorine-initiated reaction of tetrafluoroethylene with oxygen, in a liquid phase at low temperature, leads to almost quantitative yields of polymeric perfluoroethers made by CF2CF2O and CF2O units and containing variable amounts of peroxy bonds. This chain reaction is studied in a series of semibatch experiments, and the results are interpreted on the basis of a rather simplified reaction mechanism involving a sequence of elementary steps of different free-radical species. A most unexpected experimental finding is the positive action exerted by the oxygen pressure on the initiation rate; this effect is attributed to a competitive reaction of fluorine atoms with molecular oxygen to form FO2 reactive species which are able to produce a substantial number of chain-initiating biradicals. The kinetic relationships deduced from the overall reaction model are proved to fairly describe, in a quantitative way, the correlation between the operating variables and the various polymer structure indexes. The values of the typical kinetic parameters of the process are estimated; they appear to be consistent with an emerging general picture of the reactivity characteristics of the different perfluorinated oxygenated radical species in the condensed state.
Membrane-targeting peptides for nanoparticle-facilitated cellular imaging and analysis (2015)

The controlled delivery of nanomaterials to the plasma membrane is critical for the development of nanoscale probes that can eventually enable cellular imaging and analysis of membrane processes. Chief among the requisite criteria are delivery/targeting modalities that result in the long-term residence (e.g., days) of the nanoparticles on the plasma membrane while simultaneously not interfering with regular cellular physiology and homeostasis. Our laboratory has developed a suite of peptidyl motifs that target semiconductor nanocrystals (quantum dots (QDs) to the plasma membrane where they remain resident for up to three days. Notably, only small a percentage of the QDs are endocytosed over this time course and cellular viability is maintained. This talk will highlight the utility of these peptide-QD constructs for cellular imaging and analysis.
A semi-automatic relative calibration of a fixed and PTZ camera pair for master-slave control (2011)

A PTZ camera has the capability to cater to a much larger area of coverage when compared to a fixed field of view (FOV) camera. However, to utilize the full capability of a PTZ camera, it is necessary to have analytics to support event based autonomous camera control, such as automatic tracking of moving objects (people and vehicles), and zooming on to a face or car license plate to get a closer look. This is achieved by operating a PTZ camera in tandem with a fixed camera or a single PTZ camera operating stand alone under a master-slave control mode. One critical requirement of master-slave control operation is establishing a relative calibration between the master camera view and PTZ camera orientation parameters (pan, tilt and zoom angles). This paper presents a semiautomatic approach for solving relative calibration between the master and slave camera pairs that can be used in field with minimum effort.
Association of Gingival Crevicular Fluid Aspartate Aminotransferase Levels with Histopathology during Ligature-induced Periodontitis in the Beagle Dog (1991)

Previous investigations have shown a clear association between the presence of the enzyme aspartate aminotransferase (AST) in gingival crevicular fluid (GCF) and clinical evidence of periodontal disease in humans, as well as in the beagle dog model. This paper describes a 26-week study that uses the beagle dog model of ligature-induced periodontitis in which GCF-AST (corrected for collection time) was correlated with microscopic evidence of tissue destruction in the periodontium at the sites of fluid collection. GCF and clinical data were collected at baseline, at optimal gingival health, during gingivitis, and after ligation. A cross-mouth design was implemented so that six premolar teeth in each dog were ligated for periods up to five weeks. Formalin-fixed tissues from the sites of GCF collection were prepared for light microscopy and evaluated for the presence of epithelial ulceration, bone resorption, and inflammatory cell infiltration. The relationship between GCF-AST levels and microscopic findings was analyzed by calculation of sensitivity and specificity and by plots of Receiver Operating Characteristics. These data revealed a correlation between elevated enzyme concentration and microscopic evidence of disease activity. Taken together with human studies, these results provide support for the use of AST as a marker of periodontal disease progression.